This has been an intermittent problem for some time but has recently become more of an issue. With no apparent pattern, Squirrel is occasionally losing driver and alias configurations. After a lot of research, I've found that the SQLAliases23.xml file and SQLDrivers.xml file in my user profile are being renamed during shutdown to end in a tilde (~) and then being replaced with the default version of the file at the next startup. This is happening to multiple users at my location and is becoming quite a problem.
Affected versions are 3.2.1 and 3.2.2 under JRE 7 and JRE 6.