1) You MUST log off wow before uploading. If you don't, it won't have written the file to the hard drive.
2) You MUST shut down cleanly. If you ALT+F4, WoW Crashes, or your computer shuts off or some other unexpected thing happening that prevents wow from shutting down cleanly, then the snapshots from that session of wow will be lost.
Unfortunately, those are limitations of WoW's addon capabilities.
Yeah this is a real problem I wish blizz would address. I have begun digging myself in this as it really causes problems for both CTRA and GRSS when wow crashes. In this event we usually have atleast 2 raid officers tracking things. I'd love to find a way to commit things without having to log out. One thing I started doing is a /console reloadui after every boss. This sadly is the only way to force a commit as Chops had pointed out to me in an earlier discussion.