Based on the information here http://helpnet.flexerasoftware.com/isxhelp22/helplibrary/UpgradeConsiderations.htm
in particular "Therefore, you should change the package code for each build."
How to change the Package Code?
I don't have LE installed but in other versions of InstallSheld that's the default behavior unless you disable it. The only time I would intentionally disable it is some build reproducibility exercise. LE probably just doesn't expose it as an option.
Build 2 MSI and look at them using ORCA (Windows Installer Database Editor) and look at the summary information stream of each to confirm.