[OneTomcat]

Found this in one of Bill's post:

First, we have added the capability for customers to be able to update ONLY the firmware in their unit without having to overwrite their custom calibrations. This should simplify things for everyone and they can stay on top of the latest features and fixes without any difficulty.

Here's the caveat... If you have custom files that were made BEFORE 11/20/2008, they are NOT compatible with the new firmware and must be rebuilt before updating. Let me make this clear, DO NOT UPDATE THE FIRMWARE if we did your files before 11/20/2008! There are 3 new files added to the latest builds that are required for the firmware to work correctly. If you would like to update to the latest firmware, please e-mail us or call us and we will rebuild your calibrations and set up a Targeted Download for you which will include the latest firmware. Once your calibration is updated, you'll be able to select [Firmware Only] upgrades from the Gryphon Update Manager to stay up to date.

Don't know if this applies to your situation but if your truck is driving different you may have overwritten your custom tunes.