The original problem presented in the first post has been occurring for me since around SVN 1500 (possibly prior). The number of new messages field next to the folder (ie: Inbox (3)) does not always update when the files are marked as read. A manual refresh fixes this. Furthermore, sometimes the messages are marked as read, the number is correct, and then after an automatic refresh it goes back to being incorrect again. To make this more clear, here is a hypothetical timeline:
1) Log into roundcube. 5 new messages as reflected by "Inbox (5)" on the Firefox tab, Inbox (5) on the roundcube folder display, and 5 new messages.
2) Read/delete/mark all new messages.
3) RC automatically refreshes and everything reverts back to "Inbox (5)" with no new messages.
4) Manually refresh, problem fixed.
I do not have RC caching enabled in my config file, and I have Firefox caching disabled by the Firefox DNS Cache add-on.
Edit: Ignore this. I am running the latest SVN (not release)