PCMSCAN only has a few parameters selected by default to be data logged. To view or change the PID selection, go to the Settings tab and click on PID Config. From this screen you can select any PIDs you would like to data log. Just make sure that the PIDs you select are actually supported by your vehicle, otherwise they will not be logged.
I also noticed that your vehicle has two control modules in it (one for the engine, one for the transmission). This could be the reason why PCMSCAN and the other software are showing different results - since both control modules will respond to the same request, one program could be getting the response from the other control module. In PCMSCAN there is actually a setting to let you choose which one should be the primary control module. You can view/modify it from the OBD-II Settings tab.
If you still see some inconsistencies, you can send me a techlog (PM me for instructions) of the problem and I'd be happy to look at it and see if I can figure things out.