So I've been searching and searching the web for a solution and even with SPAD I was having issues with the frequency knobs and it was driving me crazy. It actually seemed that the more I used them, the worse it got. At one point, I went the leobodnar route but unfortunately, once assigned, the encoder would only operate the specific setting it was assigned to and changing the assignment knobs on the saitek panels of course would still have the same issues as before with their frequency knobs. I didn't want to install a knob for every single setting I wanted to change so that was out of the picture.
In the end, it may not have been the cheapest solution but it works so well, that I haven't looked back since installing it today. A small outfit called MotiveMods makes a kit that replaces the frequency knobs on the radio and multi panel for a solution, which preserves all the oringinal functionality of the panels using the original saitek drivers. Now, one indent actually means one frequency, NAV, etc change rather than some ambiguous number!
If anyone has been as frustrated with the saitek knobs as I have been, I'd suggest checking out the site: http://www.motivemods.com/Flight-Sim-s/888.htm
Youtube video of it in action: https://www.youtube.com/watch?v=mc_NUn2wTwg