Trauma - pretty sure that's not the correct software for the Panigale. Was it you that received the wrong CD with the Tuneboy kit?
Personally I'd delete them all from your computer and start again! PM me your email address and I'll send you a link you can download them from. Might take a while as I'm away at present.
From memory I think there are 3 programs you should have
- FlashMitsubishi
- TuneboyTrim
- CruisePreflight
The FlashMitsubishi program is the one you use for unlocking the ECU and uploading the Tuneboy software. It's designed specifically for the Panigale, Diavel and Multistrada. Don't download from Tuneboy website as it's the wrong one (or used to be). Also you'll need the user ID (your email) and password (I had to email Tuneboy for this) to generate your 'key' to unlock the Tuneboy software.
TuneboyTrim - used to adjust the fuel/ign, reset service indicator, change DQS kill time etc. all the things that Tuneboy let you adjust.
CruisePreflight is a simple program used to check that both brake levers and the clutch register correctly for cruise control disconnect. Worked on mine for the clutch, not brakes. On the bike the CC disconnects correctly with both.
Did you get the cruise & tune package?