It appears that something changed in 2.0 that all attached drives get scanned, including USB external. I don't know if this was intentional or not, but I know it isn't configurable.
Windows Defrag and Diskeeper, as well as other Defrag utilities, have different detection and arrangement strategies, so one program will report all is well and the other will report that the drive is heavily fragmented.
Personally, if you are happy with your 3rd party defrag, ignore the OneCare report from Tune-up and keep your fingers crossed that we can turn it off one day as has been requested many times.
-steve