I think I’m gonna have to call this as a bug in Blender.
I got the educators licensed version of Maya today and successfully imported the Collada file into Maya.
Also the FBX file that I used to create the 3DS file (using autodesk’s convertor) worked.
Maya doesn’t open 3DS files, so I couldn’t test that.
I created a Autodesk ASCII file in PFTrack - and that worked in Maya too.
I even exported a Collada file from Maya of the scene and tried to import the file into Blender, but again it would not load correctly (the camera and tracker nodes are present, but the camera will not animate).
So for now it looks like PFTrack 2011 will not work with Blender.
Thanks for reading along!