The problem may be in the shell that is being used by IIS to run the process -- I'm only guessing here, since I have no contact with any version IIS. If one of the differences between IIS 5 and IIS 6 is the nature of the shell used to run sub-processes, it's conceivable (though stupid) that they would choose to disable pipeline commands.

If you're using sub-shells to run utilities that talk to a general-purpose database (like oracle or some other ODBC-capable server), you might consider using the DBI module and connecting your script directly to the database. It would mean replicating in your perl script the queries that are implemented by the current command line utilities, but this might enable a lot of possibilities...