In the 2010 version I've never had this issue.
I took a screenshot of my disabled startup items in the 2010 version.
Then I enabled the disabled items and rebooted.
Next I uninstall jv16PowerTools 2010 and installed the new 2011 version.
I then attempted to disable the same startup items from before but their status doesn't change.
The program says "done" for each item and there's no error message.
The item remains enabled even after a reboot.
I've tried numerous times with this same result.
I'll have to go back to the 2010 version until this is resolved.
Windows 7 x64
Quad core Intel processor