I'm using the latest 3.11.1 on Ubuntu 15.04 (vivid) and I'm seeing some weird behavior with my Inbox. Occasionally, when I mark a message for deletion (Move to Trash, Ctrl-D) and then Tools->Execute, the message doesn't actually go anywhere. No matter how many times I Execute, the message just stays in my Inbox folder. I know it's still there because I can see it in other MUAs that talk to the same IMAP server. If I visit a different folder, or a newsgroup, Claws will notice that the deleted message hasn't been moved to trash and it will prompt me to take this action, but even if I do, the message doesn't get moved. However, if I Unmark (U) the message, and then re-delete it, then execute, it usually gets moved to Trash this time. It doesn't happen to all messages, and I've yet to recognize the pattern for which messages do get deleted (the majority) and those that don't (the minority). I don't yet have a reproducible test case. "Move deleted mails to trash and expunge immediately" is set, but I think I've had this set for forever and Claws still seems to DWIM, namely ctrl-D marks the message for deletion until I explicitly Execute. It's certainly worked this way (without the problem described herein) with 3.10 and for a long while before that (going back at least to 3.8).
Interestingly enough, running CM under --debug in a terminal, I've been unable to observe the problem. It definitely happens when CM starts up "normally" (i.e. via some desktop launcher), but so far not under --debug. Not sure if that's a helpful data point or not.
What does environment contains in a terminal and what does environment contain in your default desktop?
I don't know that there's anything different in the two environments that would affect CM over IMAP. Is there something in particular you're looking for?
Another data point: running CM in a terminal *without* --debug does exhibit the problem. Maybe --debug introduces some significant timing differences that avoid the problem?
I've seen the bug now even when running with --debug, though the output didn't show me anything that jumps out at me. One observation: it seems like if I have a bunch of messages deleted, and then CM scans and finds a new message in my inbox before I hit 'execute', the deletions do not happen. If no new messages are found between the time I hit 'd' and execute, then the deletions happen.
I have/had the same reaction, when moving or deleting a message in a IMAP folder - to another. But this behaviour only occurs in one of 2 mailboxes, i used/configured. When i use --debug Option on startup and look at the output, i can't see any error message when i delete a message and it still stays in the folder. Only the message "main.c:895:The name com.google.code.Awn was not provided by any .service files" was a little bit strange, because i don't knows from where it came. I don't use this. But when i use "Tools -> Delete" (Extras -> Löschen) or STRG-E, then all the messages, which was marked as deleted, gone away in the folder.
This still happens to me all the time. About the only thing I can correlate it to is having a bunch of messages marked for Move To Trash, but then another one comes in before I hit Execute. CM talks to two IMAP servers: Google's and Dovecot 2.0.19 on Ubuntu. The problem never happens with Google's servers, only Dovecot. I often have multiple MUAs open on multiple machines, including CM and Apple Mail.
I did some further debugging a while ago and forgot to update this bug. I think it was a Dovecot bug. In /etc/dovecot/conf.d/10-master.conf (this is on an Ubuntu system), there's a vsz_limit which defaults to 256M. Bumping this to 512M seems to have solved the problem. As per the comment above that, I "have huge mailboxes" :)