Now that I have a minute I'll respond to each thing:
In your first post- 1) I've never seen that happen before, and I can't seem to replicate it. Same as 2) I can't seem to replicate that on my end. I wonder if that's because I have preexisting saves? It should allow loading but not saving in the prologue. I'll see if I can find any possibilities for that issue. 3) I fixed, but I believe I have yet to upload that build.
Second post-
About #2- There should be an option in the options menu to disable gamepad mode. It's odd that you can't see the cursor, but if you're able to see the buttons highlight maybe you can find your way to it? I'll see if I can fix the issue with the cursor not being visible on my end.
Regarding #1 I think I found that problem, it's an issue with achievements on non-steam platforms. That should be an easy fix, stay tuned.
For #3, I see now you mean the learn abilities menu (sorry for the confusing wording!) That is also not working on my end, so I'll fix that with the rest of these fixes.