Vista might be the problem. I had to upgrade Peachtree, Quickbooks, and Quicken amongst a lot of other programs because they wouldn't work on Vista. Another thing to try... Download the latest driver for the keyspan device and reinstall it.
Keyspan | Downloads | Select Your OS
The way I understand the PH probes to work, based on the controller that I'm building, the controller reads the voltage provided by the probe when it's immersed in the different calibration solutions. It figures out what the offset is so it can add or subtract it to/from the voltage provided by the probe when it's in use. That offset is stored in the controller. I would hope that the offset is stored in flash memory so it's retained when it reboots. In your case, maybe it's not.
hmmmmm.......
Does your controller take a battery? I wonder if it needs to be replaced....