What modifications have you done to it? I am seeing some of this due to Bulletproofing. If you are running Gingervolt and Blitz, you should not be seeing this issue. I would reflash Gingervolt. If this is because of the supercharger script, then I would remove the script, and run it again with different settings. I know in the OP for this, it is suggested that you run the script in the middle, and that running it on the higher end may cause some instability, even says so in the directions from Zeppelin. I tried running the rc5 script, but it was not friendly to my phone, so I had to remove it. We got a guy here trying rc6 and loves it, but we will see how he feels within the next week. But supercharging, bulletproofing is the only instance where I have seen the card scanning going nuts. If you tweaked the sd card in ROM toolbox, that may be the issue as well. But again, I haven't seen it, or heard of it as an issue yet.
Let us know what you have done to your phone, in a little more detail, and someone can help you out a little better. I have covered a couple things above, but that is without knowing what steps you have taken to try to improve your phone.
Good Luck.