@fledge68 I tried your beta3 and the issue with corrupted source covers seems gone, Nn problems so far.
If some cover messes up, pressing the + button on the wiimote also fixes it.
However I had an issue on my first try, because I deleted the sourceflow cache before installing the new beta3 (I thought that maybe some corrupted .wfc file could cause problems). Then when I booted WiiFlow b3 it couldn't recreate the cache files (I tried pressing cache cover and reload cache buttons with no result) and all source images were missing from my sourceflow. Instead, all my buttons showed the C64 icon from source menu.
I had to reinstall beta2, let it recreate the cache files, and then install beta3 to make it work.
@Hakaisha I can't confirm your theory, my Force cIOS version in start up options is set to 'Auto' and HQ covers is set to 'no'