It's likely that your optfs got borked. Best thing in my opinion is backup your MyDocs folder (don't forget hidden files if any) - then reflash both rootfs and eMMC and start over. If you have a recent backup done with the stock backup application, you're going to get your data and programs reloaded, too.
If you have backupmenu you could try to make a full check of filesystems before booting the maemo gui, but don't be so confident that everything gets restored in the pristine state.

Beware that Transmission has been known to be dangerous for the file system were it builds the downloaded file, especially when it is interrupted in its operation.