The following worked for me:
step 1. Turn on "Write caching"
step 2. Restart PC
step 3. Safely remove an external drive
step 4. Connect the drive again
step 5. Turn on "Quick removal"
step 6. Restart PC
after that the drive was set to the "Quick removal" and Safe removal worked again.
It seems that in Windows 7, this behavior is now generally applied to USB drives as soon as they are formatted with NTFS.
I have tried the advice mentioned here (and elsewhere) to change the device settings but they have no effect. The only thing that works is to format as FAT32 - THEN eject works even without your removal tool. But I need to save files > 2GB (TrueCrypt containers) and using only 2GB on a 16GB stick is wasteful.
We have improved forced stop mechanism in the latest beta version and now the program can unlock such stubborn drives. Anyone here is interested can download the latest beta and see if it works for him: USB Safely Remove 6.0 beta 3