I've been working with Stangguy269 on this car and have been having dealing with these issues as well. Boiling down your suggestions, here are what you guys are saying.
1) EMI - Maybe, but unlikely. It does have an MSD box, but it is installed 3-feet away inside the cowl. All of the other wiring harnesses or HP EFI boxes are separated from the MSD box by sheetmetal. HP EFI is installed in passenger compartment. Engine harness is in the engine bay and doesn't run next to the MSD box.
2) Laptop - We've tried different laptops, same problem with each one. One laptop is less stable than the others, but the software always locks up while connected to the HP EFI.
3) USB Cable - I'll swap this one out and give that a try.
4) Bad Install of SW - These were all fresh installs of the Holley EFI software. We have uninstalled/reinstalled on at least one laptop. My personal laptop is a clean install of Windows from Microsoft discs, not a pre-loaded OS and a clean install of Holley EFI. I do not have this issue when working with other EMS brands.
5) Power supply/inverter - Working directly off laptop battery, no inverter.
6) Administrative settings - True, I had to open up the Holley EFI folder so I could record Datalogs. Figured that out w/in 5 mins the first time I tried to create a datalog. This is not the issue.
7) Engine Running or Stopped - I have had this issue both when engine is running AND stopped. I can sit there with the car still, no fans or motors running and it will lock up. All of a sudden I get the spinning blue wheel of death in Windows. Requires killing the Holley EFI software, unplugging the USB cable/replugging and restarting Holley EFI and reconnecting.