Oh wow, relax buddy, it is exactly as simple as stated. I have made NO alterations to the wordpress code except to add a snipped which allows me to change page categories but that has nothing to do with the question I posed.
My website has TWO themes, a main theme and a theme which shows when posts/pages belong to the Subspace category. It is a template or a theme like any other.
I have made NO alterations to the main loop.
This is obviously something which I will have to resolve myself though, like the page categories topic, because it is obviously too complicated for you guys to figure out even though I find it surprising and I don't think the setup I'm running on my site is complicated at all. The conditional tags I'm using are strictly to display each theme properly because of how I'm displaying the header mainly but there are tags which check the category outside of the header too, all those tags are intended for is to display each theme correctly.
The question I posed was simple: what dictates the category to the main loop?
Somewhere, in the main loop, a category is assigned to the loop itself. When I first asked the question I didn't know what caused the particular category to be selected, I've now figured that part out. It appears that the decision is made based on the latest post, I found this out recently when I posted something in a category different then the Subspace category, the loop then was using the main theme. Anyways, when I have time to troubleshoot it and resolve it I'm going to post here.