You might write a script that does not use any modules but displays @INC, to make sure it is looking for modules where you think it is, and read a .pm file (open it directly, don't use it) to make sure there is no access problem on the file.

In addition to the obvious settings in the IIS admin GUI, there may be differences in the metabase. You can review this as an XML file (assuming a reasonably recent version of IIS). It might be worth having a look there to see if anything differs between the sites.