I don't know the exact steps to duplicate this, and I don't know if this is the correct place to post this. I've also found a workaround.
I opened an existing ISM file, and I think this file was created before I upgraded to R3 (not sure what I was on prior to this).
Anyway, made a couple of changes (such as version number) and went to compile a new Setup.exe but it kept failing with an error about a Move File command. While trying to figure out why this was happening even though I hadn't altered anything to do with the Move File table in the MSI, I noticed it kept semi-launching the MSI near the end of the build process, which it hasn't done before and I found odd.
I can't remember what I noticed in the build log after that, but it lead me to the Releases tab, where in my SINGLE_EXE_IMAGE I noticed that 'Build Windows App Package' on the APPX/MSIX set to Yes. I set it to 'No', and re-ran the build the process.
The build process failed yet again for the same reason, and then the I noticed 'Build Windows App Package' was still set to 'Yes'. I set it once again to 'No' thinking maybe I miss-clicked, and verified that it was indeed set to 'No', and then re-ran the build. Failed again, and this time I watched as it reset itself back to 'Yes'.
So basically I can't turn off APPX (which I don't need currently) and then build Setup.exe.
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As to my workaround: I set APPX to 'No' once more, I saved the ISM file, I closed InstallShield, I reopened InstallShield from the ISM file (double clicked the ISM file), I went to the Releases tab and verified that APPX was still set to 'No'. I ran the build once more. This time the build succeeded, and APPX stayed turned off.
So to reiterate: it seems that if APPX is ON for whatever reason, you can't seem to turn off and build. You can turn OFF, close out of InstallShield and reopen and it will now be off.
