Cave Story+ Wind Fortress Glitch

Whenever I play it and I die, the counter doesn't reset.
The only way so far to fix this seems to be restarting the game.

 

I don't think there's anything else you can do. As far as I know, Nicalis is aware of this glitch. Hopefully they plan on patching it eventually.

 

Also, along with that one,

Start A Boss rush, or the nemesis challenge, wait a little bit, quit and start up wind fortress immediately afterwards.
the time will be whatever time you quit the boss rush/challenge with additional time from the fort.