Haven't really been active on this forum much in quite some time but the so called 1.3 update does a number of tweaks to the ESM (Which can be identified.) and then a number of adjustments to the exe (Which I have no way to check.) so one possibility is that some conflicts or mods now causes greater problems than before, the above about the so called FormID numbers updated can be problematic though from what I've checked it's not done to that many "objects" at least.
There's a number of AI adjustments to the ESM or rather the so called "packages" they get that dictates what they do and how but I don't know if that's serious enough to cause problems, also a more problematic issue is that several scripts got changed again such as the global companion data so any mods altering that would need to be made compatible but as I don't have the Geck installed and instead use FNVEdit I can't see any specifics or get a good comparison of what was tweaked.
Oh right the patch process for Steam is to replace updated files, this means FalloutNV.esm is loaded later than other earlier ESM files (ESP's are fine technically as ESM's always load first.) so you might need to fine tune the load order again as you should never have any other ESM loading before FalloutNV.esm
You can see some of what was changed in this image, was done by backing up FalloutNV.esm a day before the update was set to be released and then filtering out and removing identical changes between that file and the updated one, thus theoretically leaving only the updated data, it's a bit buggy (FNVEdit is a great utility but has some drawbacks.) but it gives a good basic overview of what exactly changed, as said though I don't have the means to check the exe related changes to the game engine and what else has been done.
http://img641.imageshack.us/img641/2285/12345fj.jpg
Should anyone want it though it's likely not that useful the ESM itself can be downloaded from.
http://www.multiupload.com/U72M7G3LYJ
Just some ideas, be aware the game is pretty buggy and a bit rushed (The terrain update mod fixing holes and mis-alignments shows this pretty well as does both the patch mods merging a large number of fan made fixes.) though it should be fairly stable at least, texture mods kinda push the cache capabilities over the edge though so it'll likely crash eventually if a number of those are used, stutter remover NVSE plugin and the 4GB LAA flag patch might help a little.
EDIT: Oh right I forgot about update.bsa, I guess it's hard-coded to launch via the exe file as there's no ESP or ini update to specify it.
http://img217.imageshack.us/img217/8360/1234xe.jpg
Again I haven't compared these to see what was altered, perhaps collision data, perhaps fixing holes or missing segments or anything, that DLC like file is interesting as well, DLC4 should be the Ulysses related one shouldn't it?