Correct, LMS 3.2 is not supported on Windows 2008 R2. You can upgrade to LMS 4.0 (which is supported on R2), but that is not a free upgrade from LMS 3.x. You can, however, download a free 90-day eval of LMS 4.0 from http://www.cisco.com/go/nmsevals .
It sounds like you need to contact your reseller or account manager to see what they can do. If you just purchased LMS 3.2, you may be able to get a free or discounted upgrade to 4.0.