Amit,
RegionUsageIsVAD isn't necessarily just memory allocated by .Net. It's true that the managed objects are included in this,but RegionUsageIsVAD is essentially memory allocated through VirtualAlloc, so it's possible the memory profilers you used are correct. However, you could compare these results with what SOS (a WinDbg extension for debugging managed code) reports.
In any case, Tess Ferrandez, one of our support engineers, has a great blog with walkthroughs that will help you learn how to troubleshoot memory issues, including use of SOS. I'd start with this one:
http://blogs.msdn.com/tess/archive/2008/02/15/net-debugging-demos-lab-3-memory.aspx.
If you're getting dramatically different results from SOS and CLRProfiler then I'd consider that a bug in one or the other. :) If you find that to be the case, and have a repro you can share, we'll be happy to look into it.
Thanks,
Jon