Firefly is on a Dell 1300 Inspiron laptop. CD drive is on the laptop. FAT32 disk is an external 320gb Seagate thru USB.
Probably if you are ripping to the external disk while firefly is running, the usb bus is saturated.
You might try turning off background scans (set rescan_interval to 0), and rip to the external drive like you have been. Then do a manual rescan when you are done ripping.
I don’t think that FAT vs NTFS will buy you much, though.