There's a problem when trying to load multiple mods with manifests, which does not happen consistently with smaller mods but results in the second and later mods not being loaded at all, but replaced with the manifest from the first.
There are a few symptoms of this behavior, which I surmise derive from separate but related bugs.
If the second mod manifest takes too long to load, the message appears in the console "One or more manifests couldn't be found; proceeding anyway." and the second manifest never loads. Instead, the first manifest will be applied twice during the update step (even if the second mod originally had no manifest at all) and the mod list will be loaded with two copies of the same mod ("Updating with new mod URLs : data.js, , ").
This is generally followed by a string of warnings ("WARNING : there is already something with the id ") as the same mod is attempting to load multiple times.
This happens for mods which independently load perfectly fine, and there seems to be no problem with loading multiple mods without any manifests. Part of the problem stems from a race condition with G.modLoadT only being reset to 0 once at the start of loading all the mods, rather than for each mod individually. I'm not sure whether that was intentional, but the result is that, on my computer at least, any sort of complexity in mods causes them to be forcibly timed out even when there are not actually any problems with the files. Worse, when this happens, the last manifest that did succeed in loading is applied to (and ends up clobbering) any subsequent mods in the list.
There is a separate situation where the mods will be overwritten (the "Updating with new mod URLs" message appears in the console) without the above case; the "One or more manifests couldn't be found" message does not appear and something else is incorrectly triggering the update.