The problem of different HW ID in License Manager and IDKit application (IEngine_GetHardwareId) can be caused by these facts:
1. There is a bug in HWID generation on newer Windows systems (Windows 7 with latest updates, Windows 8) with specific kind of hard drive controllers. Please see this FAQ topic.
2. You are executing LicenseManager under different user than your IDKit application. That different user account can have different permissions, what can block access to unique hardware ID of some components of your PC. LicenseManager is executed under administrator (requests privileges before starting), but application is usually executed under standard user account.
3. Your application is executed in sandbox (virtual container) which is isolated from host computer.