Does your laptop have a native serial port? I have had similar problems with one of my laptops with an actual serial port. Had to manually configure the usb link/com port protocol. My laptop with usb only has never had that issue.
Was informed on the holley help forums that reloading the software with the holley usb connected seems to fix most com issues.
If you continue to have issues, I suggest completely removing the holley software, and the piggy backed usb/ com software. Then load the newest software and firmware from the holley website (v4).
Reload with the usb connected.

High idle speed... see what the idle motor count is. should be below 15. TPS should be "0" If idle count is lower, say "0" and idle is still high, close the throttle plate with the screw and then do tps reset.
If its higher than 15 there are more things to check. call me if you get stuck.