Linc, I feel your pain dude. I had some initial issues just getting the custom tunes to the scanner device. Turned out that I needed to format the scanner. You may want to try this - AS LONG AS YOU HAVE ALL YOUR FILES BACKED UP - including the most recent firmware, tune revision, and all tune files (including stock).
If you have an X3, this is the process to format it:
1. Start up the SCT software on your computer
2. Connect the X3 to the computer via USB cable
3. Stay on the main menu of the SCT software, and press/hold CTRL - ALT - F on your keyboard
4. A message will appear asking if you want to format the MMC device/card, click Yes
5. A second message will appear asking if you want to format the device, click Yes or Ok
6. Wait for the process to finish
7. Disconnect the device from the computer
8. Reconnect the device to the computer
9. Load the latest tune revision file you have using the "Transfer File to Device" option in the Basic Operations menu. This will take a LONG time to load.
10. Your custom tune files will no longer be on the device. Reload them using the "Load Custom Tune File" option from the Basic Operations menu.
11. Try loading either a canned or custom tune file, or even reverting back to Stock.
If you have an X2 device, the process MAY be different, but you should be able to try it. I don't think the CTRL - ALT- F will do anything if the device is not programmed to respond to it.
Other option is to email
support@sctflash.com with your issue and what you've done so far, and see what they come back with.
Good luck!