Hey, that's awesome, thanks for finding that Denbo!
I guess I missed that page while searching around for a solution to this. That link also explains why the other XBee explorer (not sure of the brand) I borrowed while trying to figure this out didn't communicate well with X-CTU. That's an easy fix too, I'll just desolder the RSSI LED or its resistor on the Adafruit boards so I can use one hooked up to the computer to talk properly. I'm only using the usual 4 pins of TX, RX, 3V3, and GND on my final circuit board, and a simple echo test on that board seems to be clear of the garbage.
Glad it was something simple after all.
Interesting that I was able to communicate via X-CTU and query/change parameters (though I had trouble updating firmware), as that link suggests it shouldn't have worked at all. Whatever, I'll borrow the desoldering gun at work for a few minutes tomorrow and I should be good to go.