Alright, I seem to have solved the issue, and boy is it strange.
It all seems to be related to the use of multiple displays. On Thursday of last week I connected to a large HDTV to demonstrate the function of my script to my superiors. I dragged the geoprocessing dialog box to the big screen so we could watch it work and return messages. It seems that ArcMap somehow and for some reason remembered the location of the dialog box and tried to project it there even after I was disconnected from the display. So back at my desk, my process was running, and upon finishing it was waiting for a response from me (basically to close the dialog box). But since it was nowhere to be seen on the current display configuration, I had no way of interacting with it. Only by reconnecting to the HDTV in our conference room was I able to see the box and drag it back into my laptop display. It now remembers the location and I can see it when running the script.
I'm not sure where the fault lies with this bug, but does anybody else have experience with it?
