I can only say that I have experienced the same with other parts of xbmc, I don't know the causes and it drives me insane. I've been going to bed at 4am the past 3 days just cussing out my computer, and xbmc.
I had emulators setup with romcollectionbrowser, I went through the whole shabang importing fanart/info/images for the over 150 games that I have. It was working beautifully and then the next day...I hadn't even touched xbmc....none of my 3 emulators worked. I then got rid of that program and used advanced launcher everything was peachy. i added a few tv shows and all of the sudden none of the emulators worked. Without restarting, I tried them as standalone applications and they all worked fine. I setup gamebrowser in mediabrowser...they all worked fine.
I add movies and only some appear, I restart multiple times and then they all showup. XBMC has frozen up on me multiple times, cpu shows 3% usage. I have had files I accidently added to movies stay there permanently despite removing all the sources and despite trying to delete them directly. Which led me to uninstall and reinstall xbmc.
Getting real sick of looking up solutions, copying and pasting code, trying to setup advancesettings xml files. Downloading cool plugins that don't work without some technical wizardry that I am just not knowledgeable enough to get working.
I'm probably doing a lot of things wrong but I just don't have any confidence that I'll get this to work in a robust and stable manner. I try a different skin and other issues come up, I update something and things that were working stop working while some things that didn't work start to work. That's both the beauty and the beast of xbmc, lots of user created stuff that we probably can't expect to all work seamlessly together without trial and error.
I've been banging my head against the wall for 3 days straight...took me 30 minutes to setup mediabrowser last night...my movies were where they were supposed to be (I have like 10 different categories with different nesting so this is no small bananas to me), all 3 of my emulators just worked.
I'll probably keep both on my computer and have a last go at xbmc this weekend. I want to setup advancedlauncher to startup mediabrowser and run the emulators from that. Or maybe I'll try to setup WMC to have the option of running xbmc.
Hope you have better luck than I. I just keep telling myself....it's all part of the "fun"...much like getting kicked in the nads is the "fun" part of martial arts training.