I have this same problem when I have Firefox on screen

. My replaygain can get down to 0.00x speed, and sit there until I maximize foobar to get Firefox off the screen. Then it jumps up to 20.00-40.00x+ :S. I don't know what the problem is, but it seems to happen randomly. I have 1GB of ram, so shouldn't be a problem I don't think.
Try doing your operations with NOTHING running except the necessary files (AV, firewall etc) and foobar maximized. See if that increases performance? Also, when trying to update two of the same files (or different ones) at the same time, I get slow down also. Like if I replaygain 1 file, while playcount updates another. It lasts for a few seconds, then goes away.
Just trying to cover all bases so the root of the problem can be found for you

.