Rick - concerning your XML and blank line information: I understand your description, and can see the test script results, but I am still at a loss to explain. I've looked at every single file in the /forum directory that has been modified (by date), most of them still carry the install date. The ones that were changed, I tried defaulting to previous versions, or removing (like you did for the header), to no avail.
Just for my understanding, when I go to UBB.Threads community, for example, and look at the source - there is a blank line at the beginning as well. When I go into a forum on that site, there are two blank lines in the source. This seems to match what I see at Penny Profilers.
I checked our domain control panel, there are no cron tasks or compression items that are apparent.
Any other ideas?