(This is not related to IKVM.NET, but since I spent several hours tracking this down, I thought I'd write it up here in the hope anyone else struggling with this will find it.)
One of the lesser known (development) features of the CLR is the ability to override the regular Fusion assembly loading rules by setting the DEVPATH environment variable (and adding an entry to the machine.config to enable this).
It turns out that this feature can be disabled by setting
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Image File Execution Options\DevOverrideEnable to 1.
When the IE9 Platform Preview is installed it adds this value to the registry.
To re-enable DEVPATH, set the value to 0 or delete it.