Alright, so I got it to work. I'm going to provide some instructions since this seems to be an issue for many.
--- Try these steps first ---
1) Make sure the tuneboy cable is connected and recognized by your PC. I also had the ignition turned on, not sure if this is necessary.
2) Run the TuneBoyUpdater.exe program.
3) In the dropdown, you should see something there. Select it. I don't recall what it's called but there should only be one.
4) Click the Upload button, then select the .hex key that is included in the zip. (As of this writing, it is called "TuneBoy_Microcode_6_12_18.hex")
5) Follow any prompts. This is very fast and takes less than 5 seconds.
6) Try flashing the bike as per the instruction manual. (this fixed it for me)
--- If those steps don't work ---
1) Go grab the files I've dropped
here on my google drive. (This will remain for as long as I remember)
2) Follow steps 2-4 from above, but instead of the original hex file, use the following files:
a) start with "TuneBoy_CAN-M4D_Fix.hex" file, then try steps 5-6 from above
b) if that still doesn't work, use "TuneBoy_CAN_M4D_Fix1.hex", then try steps 5-6 from above.
If you're still having issues, email Wayne for assistance, then feel free to PM me or reply here. I can help however I can until Wayne gets back to you.
Please reply if any of this worked and helped you, and which file ended up doing the trick. Big thanks to CristianRus for providing me the files, and DerekJ (from a FB ducati page) for all of the help!