I had a very similar problem on my first SVT.
Try this:
The white "F" shaped plastic mounting bracket that you bolt into the frame serves as a ground of some sort......on the inside of the "F" there is a metal piece that touches your ECU when you complete the install. For a quick test, unscrew the bolt from the frame just enough so you can turn the bracket so the open end is facing you.......the put like a piece of leather or thick cloth over the ECU (or on the inside of the bracket)and wrap it lightly with electrical tape (or on the inside of the bracket) so as to prevent the metal from touching the ECU......
I came up with this because I had absolutely no problems with the chip and then one day I had to take it in for warranty work and pulled it out. Upon re-installing it I put the Diablo Sticker back over the chip and the ECU, I scraped part of the sticker off thus exposing the metal on the box of the ECU and I had problems every since.....until I eliminated the metal to metal touch of the bracket and the ECU......
I posted on this back in 02 or 03 and I don't think anybody every answered.
Chime in here any time guys!!