Hi tlgroons and welcome to the forum.
It's hard to say what happened with your OS4.1. Perhaps some program you installed as last messed up with Devs:Monitor driver?
Or do you remember changing anything in WinUAE emulator settings?
The thing is that FlowerPot is just a smart installer of OS4.1 system on your Windows, Mac or Linux. That means if you managed to run OS4.1 and boot to its desktop, then FlowerPot did its job already, you know.
Anyway, I am sorry for the inconvenience. Maybe try googling the issue you are exeriencing or ask OS4 users at www.amigans.net