Hey Bob.
If you are disabling the WAI link track function under utilities/Presonus faderport its usefulness is severely impacted as the motorised fader does not move with track selection. On the other hand if you are talking about the WAI setting under preferences/control surfaces, that is only the colour indicator showing which track is currently being controlled, so it will have no adverse effects on the faderport functioning. If disabling only that has fixed your issue, problem solved:) If it is the first I certainly encourage you to explore further!
I found consistency is paramount in getting the faderport to work correctly, and one thing that certainly helped was to ensure that the faderport was last on the list of both midi input and output devices, and to ensure that once set the order never changed. This setting is in the ttseq.ini file, located in appdata\roaming\Cakewalk\Sonar Platinum. Open the file in a text editor and the I/O order is located at the very bottom of the page, the LAST two numbered sections labelled 'midi in device map' and 'midi output devices'. Just cut and paste the device names after the '=' symbol to reorder them so that the faderport is last. Once you have them set either make a backup of the file in case of future problems or set the file properties as read only so that Sonar never reorders the devices. Just remember to change it back temporarily if you ever add any new midi devices.
The other thing, that you probably have already done, is to check that both key after touch and Channel after touch are enabled in preferences>midi>playback and recording.
Unfortunately for me at least there was no way around resaving projects with the Faderport enabled and working, even after setting the ttseq input and output settings, but it certainly fixed the same issue you are having on my system and the faderport has been ticking along for a couple of years now.
if a project still won't load even when you move the fader, remove the control surface, then load the project and add it back in before saving.
As tedious as all of this is stick with it Bob - it is such a handy device and works transparently once it is behaving!
Other than that no doubt others here will have good ideas, and with a little luck Azslow will be along sometime soon and there is nothing he does not know about control surfaces:)