Build Verification Issue

I have two sets of files:

1) Some Setup CDs generated from various Visual Studio or Borland C++
projects.

2) The projects (and source code) used to generate the Setup CDs.

I also have instructions to configure the projects, the Setup Wizard or
Installshield application to generate the Setup CD images.

****** GOAL ******************

I need to verify that the projects ( and source code) is indeed the
ones used to generate the Setup CDs I have.

***** PROPOSED METHOD ****

Rebuild the projects and then use some kind of file compare tool to
check file equivalence.

***** POSSIBLE ISSUE *************

I have heard, that compilers (or linkers), or the Setup
Wizard/Installshield may put a timestamp in
their output files that may cause problems in my verification method
above.

I have seen on the internet that the Microsoft Installer uses
file-modified timestamps for file versioning rules (whether to replace
a file during installation).

**** QUESTIONS **********************

Can anyone verify the timestamp issue above?

Can anyone provide advise or a solution if there is an issue here?

Thanks In Advance,

Scott