I still haven't figured this one out. I did have a rare issue where the game would freeze while the YouTube scanner was working and indicate it was "not responding", but it would unfreeze itself after a short time. I tried to inspect what the game was doing while frozen but have not yet been able to find the problem. I did make some changes in this latest version to the YouTube scanner that might help or might not change anything with this bug. The bug is very rare for me but you seem to get it a lot.
Because the mod manager is so crude and simple to actually see the changes you'll need to click the "Remove Mod Loader and Mods" button to remove the old mod loader and mods and then click "Install Mod Loader" to copy the new loader in. This is how every update will be until I come up with a way for the mod manager to know if an old loader/mod is installed.