Behold- random hypothesizing on the nature of the metaphysical in the 40k universe, complete with a few ideas stolen from very intelligent nerds and a side of ketchup.
First and foremost, I feel I must define the basis of my little tirade.
What is the warp? The warp is the world behind the world. It is a dimension beyond the three we are familiar with, one that has connections to ours but is forever separated from it. It quite frankly is incomprehensible in is true form, as least as mortal minds are concerned. We must ascribe mortal properties to something that is immortal, or give it mundane relationships in order to abstractly grasp its magical potential. The bridge between the material realm and the immaterial one lies only in the soul.
What is the soul? The soul is a connection between life and the the empyrean. While it is not necessary for life, or sentience for that matter, to possess a soul, it is only through the soul that life can influence and even manipulate the energies of the warp. Souls, when present, are "colored" by emotions, and the most important effect this engenders is a "coloring" of the warp itself. That is to say, where a concentration of souls with powerful emotions is present, the warp reflects these emotions. Most souls can only influence the warp. It takes an incredible willpower and intellect to even attempt manipulation of warp energies, and for the overwhelming majority of sentient life in the galaxy, this is obviously beyond expectations.
So, where to begin?
It is often said that the warp is timeless (note I did it in this blog's very first post) and it is completely ignorant of our laws and theories of physics. I do not believe this is entirely true, or that it fully explains the situation.
By using the warp as a method for faster-than-light travel, it must have some sense of temporal and spatial relationships. For example, if this were not the case, considering the chaotic probabilities of the warp's nature, summoning a demon or conjuring the effects of a spell to your location would be functionally impossible. The energy is as likely to appear on the other side of the galaxy (not to mention 32,845 years after you die) as it is in the functional here and now.
Speaking of the sides of the galaxy, when considering the notion that warp energy shows no signs of influence from outside this galaxy, and the notion that there are almost without a doubt countless other peoples inhabiting the universe, the likelihood is that we see only a part of the warp. This idea requires the acceptance of the theory that there are "parts" of the empyrean, and that they therefore have some spatial relationship to each other.
In terms of time, I believe the warp must adhere to its advance at least partially. Souls and their emotions are present in the here and now. They are tied to mortal bodies and consciousnesses that are subject to the progression of time, and in a bastardization of the Heisenberg Uncertainty Principle, time must have an effect on the warp if the connection exists via the soul. Just as the warp can enter the material realm and influence localized time, so too can time influence areas within the warp.
I then ask myself how does this relate to what happens in warhammer 40k? Well, let's look at faster-than-light travel. A ship fits itself with crew and cargo, and (in the case of any concerned civilization) heads far enough away from any local population so that the energies unleashed in transference between dimensions does not have unwanted side effects. The ship enters the warp and begins traveling towards a destination. This is an incredibly important point, because it requires both a direction and points of reference, which can only exist with some adherence to both time and space. Moreover, in the case of Imperial ships, the Astronomicon is used as a sort of lighthouse or beacon for reference, and entire charts are made of calmer warp routes and safer jump points. I believe that, because souls are the connection between this world and the next, time influences the warp and does so most significantly around where souls are most heavily congregated. Likewise, whether are very few if any souls present, like say, across the vast expanses of empty space in the galaxy, time has little connection and unimpeded journies can be made extremely quickly.
Now, having put this forth, I must address those isolated incidents in which there are reversals of the flow of time. There are not many documented, and certainly travel in the warp must heavily favor a forward flow of time, or it could not be used with regularity as a vehicle for said travel. So why do they happen so sparingly, and why at all? I would say that, like an ocean, there are eddies and stagnant pools created that do not follow the flow of everything else around them. I hypothesize that there are cradles or pockets of warp energy that remain undisturbed by the flow of other energy around them. So a ship that is deposited in one of these pockets could very well emerge from the warp years before it left, or years beyond its intended arrival. Because of the chaotic nature of the warp however, these pockets are not likely to remain untouched forever, and can be destroyed, subsumed, or melded into flows of the empyrean. Obviously, the implications of this are widely unpredictable, save for their unpredictability.
I believe that there is further evidence for my theories. In the terrible book, Battle for the Abyss, a navigator describes looking at the planet of Macragge as something akin to a beacon of light, made so by all the souls. I'm sure Macragge at one point was devoid of sentient life, so if the warp was without a sense space or time, how could the navigator see the effects of the souls together and at that point in time? The Eldar, of all kinds, utilize the famous Webway for travel throughout the galaxy. Those undamaged parts are far more reliable than the warp itself, and though its geometries are certainly alien, it still is a series of tunnels at its most basic. A tunnel must pass through space and time. I could go on, but this is already a pretty long post.
It would be logical to ask what the very purpose of souls is, and by extension why we and others were created with a connection to the warp. The Old Ones are credited with creating most of the races in the galaxy, and as far as I know, all races made by them have souls on some level or another. True, a large number of those races were created with souls so that they could utilize the warp agains the Yngir and the Necrontyr, but that is besides the point. For those races made first, such as the Eldar, why souls at all? I believe the answer lies in the need for expression and connection in almost all of sentient life. The Old Ones, by granting or indeed making souls, gave the "lesser" races a way in which to commune and relate with their creators. I think the Old Ones probably felt very basic social needs, which would have been the motivation behind the imbuing of souls and the crafting of the races at all. Now, one would be justified in believing that the Old Ones did not give souls or make them. I have no evidence or mind to refute that idea, but it doesn't change much. If souls and the connection to the warp are simply products of natural processes alone, than the Old Ones surely knew this and, armed with said knowledge, made the races anyway. Whether desiring kinsmen, worshipers, toys, or whatever, the Old Ones made creatures that could connect to them on both the physical and metaphysical level. This, I believe, is the reason behind it all.
I apologize for the lack of thorough organization and substantial evidence, but for those few who read this I hope you give some feedback and take what you will.