It might well be due to a reboot, but there the question is if you do suppress the reboot or not?
Also, if I get this right, the scenario is:
Job 1 executes and where no appropriate .NET is found, it exits with a defined error code and calls another job;
Job 2 installs the .NET and then calls Job 1 again?
Question, why don't you simply add a condition into the job checking if .NET is installed and if not, include it into the one job? That would be simpler and easier to handle I guess.
-BBC