This guy decided to do a Windows vs. Linux test.
His department takes Microsoft's money. No matter how much you spin, you can't deny that fact.
Now, he could have avoided the appearance of impropriety by getting someone from the Unix department to do the Linux part of the test, but he didn't.
And he can't claim that it didn't occur to him that there might be an appearance of impropriety, since he's been publicly called on it (and responded to it) before.
Very simply, the test may or may not be accurate (we don't know because the only thing published thus far are the results, not the methodology or testing criteria) but it's tainted by his connection to Microsoft dollars.
The only reason to go ahead and run his test would be to make the grant givers at Microsoft sit up and take notice of him.
Well, that and to give you shills some another tainted report to crow about.