Were you using a different OS before? (As it worked before the re-installation on a different workstation, trying to nut out what is different between the two) Are there any differences in the user account / WinGate version / etc. since when it worked and when it stopped working?
If the differences are not readily apparent, I do know that version 6.0 has better support - you could consider upgrading. Version 6.x can use your existing 5.x key, you get all the benefits of the bug fixes, but not necessarily all the version 6.x features. (Depending on when you purchased your 5.x key) It is also available on a trial license, so you can see if it does what you want it to do before upgrading ...
Before upgrading though, check which features are available on which key types (
http://www.wingate.com/wingate-licensing.php)
From the release notes:
8. A number of enhancements to WinGate's user database integration with the OS NT database. These include:
Greatly improved enumeration of large (12,000 plus) user databases on remote AD servers or domain controllers.
Improved control over when to synchronise with the OS user database.
GUI for specifying remote AD server or domain controller for synchronisation
Support for plaintext authentication to a remote user database.