I had an issue today with installing assemblies into the GAC through installshield. My installer has several components configured with a Destination of [GlobalAssemblyCache] which is the recommended way of performing a GacUtil through installshield. Now previously, the ".NET Scan at Build" property for these components had been set to "Dependencies and Properties" and everything worked fine. Recently we have been updating the installers to work for 64 bit installations (managed by altering the ISM as part of our build process). As a result of this I had to remove the dependancy scan as this was causing issues on 64 bit servers. I set this field to "None" and soon found that all the assemblies I had targeted at the GAC ended up on the root of the install drive (i.e. c:\) instead of in the GAC :o
Anyway, I eventually managed to solve this issue by setting the ".NET Scan at Build" property to "Properties Only". It seems that this has to be set for GACed assemblies as it causes the MsiAssembly table to be populated.
Hope this helps anyone else with similar issues.