Well ideally when you install mods none of them should be conflicting with each other or the vanilla game even because they're supposed to be intentionally separate from the game files so as to not corrupt things. Some mods though use different installation methods which will make them incompatible with others, though I don't believe any of the mods currently available to download here on T3A really have this problem much. I think RC mod has a very unique install but I can't think of which others might.
In addition to that, it's likely that perhaps you're just not used to the zoom settings. In our recent patches and special goodies we've been doing here one of the things was widescreen support. If you are using a widescreen monitor, widescreen resolution, and the widescreen map pack, then yes your default zoom settings are going to be very very different when you're playing a mod versus when you're playing vanilla. The reason for this is because almost all of our mods were developed specifically for the Official 1.03 patch. We've since then gone beyond that patch and started doing our own, but as a standard mods are still made off of the 1.03 so that people aren't forced to use unofficial content just to run mods.
A solution to this problem would be to go into the maps that you're having issues with and edit the zoom values and save them as replacement maps.Go to the full post