Okay, so I moved the current install dir to a tarball and recloned the program. This gave me a fresh start on 2.1.4.
Everything resetup fine, as expected. The new unified installer is awesome.
I am remote right now (at work) and wanted to test it out. I ran the test all station program, 1 minute a zone from my phone and then closed the browser. Since I have remote access to the OSBO, I ran a tail -f on todays log. All the zones cycled (in the log) as they should have on the minute mark. If it was in the log, I can only assume that the zones switched correctly.
Sadly, it is supposed to rain for the next couple of days, so I wont see the system start on, but it should at least log a rain delay.
I am very optimisitic that the re install of the software fixed the issue.