Can't say I've had any problems with mods so far and I haven't even touched the archiveinvalidated file. I'm running about 2 dozen mods. Usually the red exclamation is due to missing meshes/textures, so just make sure you've copied every file in the archives you've downloaded into the correct location.
Also, someone has just ported the FO3 mod manager to New Vegas over at the Fallout New Vegas Nexus. Someone else is working on a full-fledged NV manager, but for now it does the job. It has options for archiveinvalidated.
Good let me know when the one fer NV is done.