For the record, should anyone come across this thread via a Google Search, my issue is actually not resolved. While everything was working during my previous test, subsequent ones reveal the same issue.
Though I never had issues before installing the Toolbox script, but cannot tell if this issue is related to it or not. Every time on startup, Pix is installing 62 modules and takes around 60-120 seconds to actually get up and running. Once it is up, it does not behave correctly and nothing works (open images, auto STF, even changing preferences).
I am not intending to derail this topic, but I can't make heads or tails of what the root issue is. Curiously, I have found that restarting Pix results in significantly faster startup and everything seems to work fine. That seems to indicate that something is going wrong during the first start up for a given PC wake session, but have zero idea what that could be.