Thats a huge discrepancy.
Just guessing but I suspect it may be to do with the file sizes that each "considers" to be a fragment.
Vista's standard defrag (not run from cmd.exe I think only counts anything under 64mb as a fragment.
If you run from command line you do have the option to defrag all file sizes... something I have done many times, and the new detailed report then shows no folders fragmented etc.
I found with command prompt report that sometimes the headline figure varied wildly, as high as 9% fragmentation (still say's defrag not needed) and if I check again a couple of days later it was back down to 1 or 2% (auto defrag turned OFF).
After a clean Vista install (following a problem that all began with someone asking about a defrag defrag problem unbelievably) I am letting Vista run defrag on a schedule and will see how it performs.
And it all started with this :)