Hey there, very sorry to hear you are having issues with the ending. Its been two years since I've updated the game, so I don't remember exactly what is causing that bug but I certainly remember a few people experiencing it and thought we had patched it. You are probably right that it has to do with save data, but deleting your downloaded folder won't actually delete that information because the saved info lives in another location. On windows you can use the Registry Editor to locate it: \HKEY_CURRENT_USER\Software\bubbles\Little Bug. Deleting that folder will get rid of the save data, which means all data will be lost but the bug will probably be solved. Also this folder contains saved information and may need to be deleted: C:\Users\user\AppData\LocalLow\bubbles\Little Bug
I know its not ideal to delete all saved data, but its the only solution I can think of at the moment.
As for the ending, I thought I'd share why it is how it is: Hard agree that it needs a checkpoint after the first 25 seconds. The simple reason is that Little Bug was my first game and I didn't have the skill/time to make the animation of the momster start at wherever it was when you hit that checkpoint. The simple solution was to make it start from the beginning of that animation everytime. It was one of the last decisions I made before publishing the game and if were to ever patch it I would add a pause feature and a checkpoint to that last part. Let me know how it goes and thanks for your feedback!