Not sure if this applies to your situation... but be aware that when you execute an ASP app in IIS that IIS may make temporary copies of the dlls that it thinks the app will need. It will load those dlls instead of the original ones in the ASP app's folders. However, when you have .net wrappers around native dlls, the way that FDO does, IIS may not actually copy all of the native dlls it needs to that temporary folder.
You can put all of the FDO dlls in their own directory someplace and then add that directory to the start of your system path. Then IIS will be able to find them. However, this may cause all FDO-related apps on your server to use those same dlls. Hopefully that won't be an issue.