Rather than the wait cmd.exe any other method did you tried like-
Dos C:\swsetup\MSProjectProOnline\setup.exe /configure C:\swsetup\MSProjectProOnline\Project32Configuration.xml
Wait cmd.exe /c cd C:\swsetup\MSProjectProOnline && setup.exe /configure Project32Configuration.xml
Running through batch file, like
Createfile until EOF
setup.exe /configure Project32Configuration.xml
MOVE __createfile install.bat
Wait cmd.exe /c install.bat
You can also use steps with current user settings like in your 1st execution action.
However as @JasonWalker mentioned your steps seems correct but something is not working from os prospective, if your setup is working locally without any special arrangements it should be working without any issue from BigFix.
I have seen many cases where some parameters is required as pre set which sometime missing while running it from BigFix is not looked properly. There could be other conflicts related to access on the machine, pre req of any which might not come in light till now, could be that machine have some os issues etc.