Yes, since ISAS 3.5 was packaged quite a bit before Windows 2003 it is possible that there are older components included which will conflict with newer versions on the new OS.
Have you tried using a transform on the ISAS 3.5 package?
The easiest route to take is upgrading to the new version of AdminStudio is 5.5,
http://www.installshield.com/products/adminstudio/. As seen in the Specification document,
http://www.installshield.com/products/adminstudio/info/specifications.asp, Windows 2003 is explicitly mentioned.