If you run the 2008 Power Tools BPA against a TFS 2008 install that has the 2005 Team Explorer also installed on it you will get virtually no reports generated. It runs to completion but the reports are empty.
This is due to some clash between the BPA and the TFS 2005 DLLs (V8.0). Removed the 2005 Team Explorer and it works as expected.
Now you are probably asking why would I have 2005 Team Explorer on a 2008 install? It is because a number of the third party TFS add-ins, such as eScrum, require the 2005 DLLs either to install or to run. As in theory the 2005 and 2008 installs are site side by side so it should not be an issue - but it is for the BPA.
In the case of eScrum the answer is to place the 2005 DLLs in the eScrum web site bin directory (as opposed to the GAC) and all seems to be fine - the BPA works and so does the eScrum web site.