I just downloaded this randomizer but it seems to work only on the original game. I made several seeds following the app instructions and tried them on both versions but on CS+ I always get the same items as vanilla game. Is there anything I'm doing wrong?

After generating the data directory, when you copy it into your Cave Story+ directory, it needs to overwrite the files *.tsc files inside "Cave Story+/data/base/Stage/". Right now the generated data directory is more set up around the freeware version, so it's not quite as foolproof as it could be. However, if you compare the generated "/data/Stage" directory to the original one, it should be fairly evident where the files need to go.

Cave Story Randomizer  version 0.6 will detect whether you've dropped a freeware CS directory or CS+ directory, and will generate the appropriate structure based on that.

Thanks for putting up with it for now and sorry that the process isn't as easy as it should be!

The aforementioned version 0.6 has been released. So please download it and tell me whether you think the process is easier to understand now! c: