Execute %TEMPDIR%\Setup.exe -s (Wait)
Delete Files(s)%TEMPDIR%\*.*

For some reason, even though I have the "Wait for Program to Exit" checked (Wait), it still deletes the files before they have totally installed the application.

Any ideas?

Contributed By: Rod Trent [MVP SMS]
Sounds like it may be an InstallShield installation? If so, installations like InstallShield "take over" the installation in its own memory space, so that SMS Installer thinks the installation completed and continues the rest of the script. Try using the "-SMS" switch after the "-s" switch. This makes the external installation SMS aware.