PF3 is much easier to use than PFE, so it would avoid a steep learning curve.
PF3 gives you the frequencies on the kneeboard after connecting (unless you use P3D, which has no kneeboard), but you may have to switch to the correct page to see the frequencies. If you tune to an unused frequency and it the zero key (top row, not number pad), then you should see a message about the correct clearance frequency. For ATIS you could check before loading the flightplan in PF3: In Options #2 there is a button do add new frequencies, but you can use that button to look up existing frequencies, too.
As to the initial problem: Sounds very much like a permission problem, but I can't give you a recipe to fix it.