ok... finally figured it out.

So, in the pins.h, under ULTRA_LCD, there are several sets of pin definitions, sitting in an IF...ELSEIF...THEN structure.
Since I was only using the NEWPANEL part of the code, that was the only place I had set the pin definitions for the LCD, the encoder and buzzer (note: the buzzer is not hooked up. This will be important in a moment).

Now, I have a touch of OCD, so, just to keep everything looking good, I went through the rest of the ULTRA_LCD and set the pin definitions to the same values for each board type. While doing this, I noticed that under one section (LCD_I2C_PANELOLU2) the buzzer was set to pin 33. Will, as I said, I have a bit of OCD. Having pins spread across AUX-4 drove me crazy, so I moved everything down by the +5 and GND pins. This put one of the encoder pins on 33. Hmmm....

I recompiled and uploaded. Low and behold, that darned thing is now working correctly. Apparently, when you pull up the menu, the program changes the panel being used. *shakes head*

So, when changing pin definitions, change it for every section of code in the pins.h.

Once I have this bugger working, I may see about making a new control code module. Less repetition, less chance to miss something. Then make a document that would give all of the correct values to put in, based on what board you are using.