Season 1 and 2 store saves in the same folder, so it's normal to see the first season's saves in the second season. As for the crash in gelery, most likely the mods screwed up the persistent file. You can delete it, but then you will lose settings and open scenes in the gallery. Settings are easy to restore, about the gallery - not ready to offer solutions, I need to look into the code. As soon as I find something I will write.
Added
To restore the scene gallery is quite easy - copy unlock.rpy to the game folder of the first season and just start the game. Unfortunately the content of encyclopaedia is more difficult to open, I have not found a quick solution.
In any case, do not completely delete the old persistent file, copy it somewhere just in case.
