Same has happened to me. It seems Flashfire / Flashpoint doesn't go with Chkdsk.
Beware trying an uninstall: last time I tried to uninstall it, I got a permanent BSOD (i.e. BSOD every time I tried to boot into windows, no way to fix it). Had to reformat the drive and install everything again.
Now I have it going into chkdsk every time again; this time, I can't be bothered to try and uninstall it (my reasoning is if I did, and had to reformat again, then it still might happen *again* on the new install). To me, the increased performance is worth having to hit a key to get past chkdsk every time I boot up.
You can edit the registry to skip chkdsk I believe, googling will probably reveal how to that, but I am definitely not going to try and do that. As I said, to me hitting a key is fine.