AFAIK database rebuild is two steps; first is fsck_msdos, second is checking every file for changes. You can check the logs yourself by installing Wampy and enabling adb, maybe your filesystem is also having issues?
Long rescan usually happens if there is a date mismatch between device date and pc. About porting rockbox - you'll have to integrate with almost all system services to keep Sony sound enhancements.
For me it's Thunderbird, "Blogs & News Feeds" section. After version 120-something it stopped resizing images on article load - this is the part I find unsatisfying. Otherwise it just works.