I've been playing V21 EXP 5 for about a week and during that time I've only found two alien bases, one small and one medium size, but after each one I never got the Xenopedia entry for the alien base itself which leads to the base upgrade research project.
Getting the base upgrade worked fine in V21 EXP 4 and I didn't see any mention of the base upgrade in the V21 EXP 5 thread. So I'm wonder if the build itself is bugged, do I need to find a large alien base, or is my game save bugged.
Something else I should mention is that I changed a few of the game settings in the config.xml and weapons_gc.xml files but that was only to change to the weapon time units back to fixed values. Either way as far as I could tell neither file had anything to do with alien bases or research projects so that shouldn't of made any difference.