Ellery,
Hmm, how are you integrating your Fusion VM Windows session into OS X, not running under Unity are you? Do you also have a functional BootCamp instance you could work from? Esri will flat out NOT answer any support issues if you are running Fusion, Parallels or Virtual Box. And of course you should be aware that ArcHydro users are expected to be self supporting--although the Water Resources team is happy to receive legitimate bug reports.
If installed correctly, ArcHydro is pretty robust under native Windows, although I'd disagree with Mark about using ArcHydro version found in the Corps of Engineers HEC served release of GeoHMS, or their GeoRAS posting. The "development" versions from the ftp site of these and the ArcHydro releases have bug patches applied as they are uncovered. Considerable delay in the patched releases finding their way back to the HEC site.
Quite a bit of installation help to ensure your ArcGIS Desktop 10 is configured correctly--one of the biggest issues being insufficient user rights elevation to fully register all COM assemblies--disable UAC on your VM or activate THE Administrator account and install from it. Another issue being exhaustion of registry resources during installation--have to pre-set registry to its maximum size (search forum for RegistrySizeLimit - 0xffffffff).
And if the ArcHydro installer runs correctly, you will have an ArcHydro entry present from the Customize --> Toolbars to use to activate the Extension. And you will have ArcHydro tools registered into the ArcToolbox with no additional configuration needed for use. Have another go at an installation, uninstall ArcHydro and then download and run the ApRegWork utility ( ESRI.APWR.ApRegWork.exe ) from the ftp site--use it to fully remove residuals of your prior installations. Then run the latest ArcHydro (or GeoHMS) .msi installer from the ftp site "Run as Administrator", or as THE Administrator of your Windows VM.
Post back if any of that is unclear, or if you follow it all but are still stuck.
Stuart