Just to be 100% sure it isnt some sort of issue with sprites in the project folder causing the issue, could you try one more thing?
Lets try cleaning up the project folder of anything that isnt being used, essentially getting rid of all trash left over files.
Could you try following this guide?
This is clear out all unused assets, clean up your project folder.
You can even make a backup of your current project if you dont like the result, but it wont clear anything important, just left over sprites from deleted objects or experiments you might have done.
With a clean project file, if piskel is still messing up, then i have no idea what could be the issue.