Hi there Ingix!
First of all, thanks for the bug report! We really appreciate you pointing us out, and we'll look into it the next few days to fix it. We assume the reason is as you pointed, the method we use to check for existing files is from the framework itself, and we'll run some tests to check if its case sensitive or not.
We are planning a new patch release (version 1.2.0) for the upcoming weeks, and we'll include this bug fix!
Regarding your question, yes, all save files are compatible in future versions! But in the worst case scenario, you could just copy and paste your solutions for puzzles you already solved (but we are confident your savefile should convert properly to newer versions of the game).
Please let us know any more issues or problems you find. We have a github page (https://github.com/MarvellousSoft/MarvInc) where you can create issues reporting bugs, request features and follow directly the development on MarvInc :^)
Lastly, did you know we are releasing MarvInc on steam April 27? Spread the love!
http://store.steampowered.com/app/827940/Marvellous_Inc/
Cheers and carry on,
Rica