I had the same problem (and have submitted a license reassignment request), but wanted to provide some information for bug fixing.
When 3.7 updated on my PC (Win 7, 64-bit) on 6/11/2011, it appeared to do so as a fresh install. I cannot tell whether the 3.7 installation correctly migrated my existing files. I'm describing below what I find on my computer as of this morning.
I find two installations of Hero Labs directories:
One is located in C:/Program Files (x86)/Hero Lab and contains HeroLab.exe (modified 6/4/2011), HLExport.exe (modified 6/4/2011), eight .DLL files (modified 10/16/2008), readme.txt (modified 6/4/2011), and two uninstall files (.dat and .exe, modified on 6/11/2011). I also have two subdirectories, which are "docs" and "product". My shortcut on the desktop is currently pointing to HeroLab.exe file contained in this directory.
The other is located in C:/ProgramData/Hero Lab and contains three files and five directories. The files are herolab.prefs (modified 6/12/2011), herolab.prefs.preconvert (modified 6/11/2011), and installerinfo.txt (modified 6/12/2011). The subdirectories are "cache", "customoutput", "data", "download", and "skins". I note that in the "download" subdirectory are "hl36g_install.exe" (modified on 6/2/2011), "hl37_install.exe" (modified on 6/11/2011), images.hl (modified on 5/14/2011), and mutants3.hl (modified on 6/11/2011).
Is it possible that having the HeroLab.exe file in the C:/Program Files (x86)/Hero Lab directory and having the data files in the C:/ProgramData/Hero Lab directory is causing some sort of confusion about whether my M&M 3rd Ed. installation is licensed?
I hope this helps with tracking down this problem. If a solution can be found to fix this without needing to send me a license reassignment, I'd be grateful for quick advice, as I have a game running here in 4.5 hours. Thanks.