just to share info - i had the same problem mr pacs had way back on the first page (install program not recognizing that the phone had rebooted).

what i ended up doing was removing the sync cable and plugging it into a different usb port on the same computer, then running the install program again. worked fine for me.

i had to do this for a couple of things, so if the software seems to not be seeing your phone anymore, try using a different usb port. might be enough to get it to look and recognize it is there!