If I understand correctly the problem was due to Fraps´save folder be located in your ´C´ drive, which are your SSDs.
Then you realized it, deleted the files, and solved the problem. I guess you have moved the Fraps´save folder to your HDD, eh? The thing is that you are going to lose quite a lot of performance by doing so. Recording times on HDD takes so much time, as Fraps records them in AVI file, which are huge files.
The best to do is to keep saving your files on your SSD to gain performance -- obviously you have to keep yourself moving the files to your HDD as soon as you finish recording.