Cost is almost the exact same for the two different systems. The AE reader (with the appropriate "enhanced package") will read ANYTHING on the supported vehicle brand up to the year it is supported through. Mine is supported through '08, and to upgrade I would just have to pay $100 for factory support to send me a new hardware disc. The SnapOn reads whatever year the cartridge is good through, and whatever the secondary cartridge is programmed for.
As far as your problem, it's really hard to say. I gave up trying to diagnose Powerstrokes over the internet a long time ago. I plug my AE in at the slightest hint of anything going wrong, whether it's my imagination or not.
You can try your UVCH connections, pull the valve covers off and see if any of them look or smell burnt. Also, anything over 3000 miles on an oil change and these engines will just throw a hissy fit worse than a 2 year old when he doesn't get something he wants.