thanks for your feedback. The main purpose of FlowerPot is to install and run OS4 on your non-Amiga computer. Regarding the issues, I am afraid they are both beyond the FlowerPot scope (and my expertise too).
I am not sure if WinUAE supports joypads in OS4 yet. Maybe you can ask the author of WinUAE directly here: http://eab.abime.net/forumdisplay.php?forumid=5
Regarding RunInUAE, I have the same recommendation - to contact its author at http://cshandley.co.uk/
and report the bug to him, and maybe to WinUAE author too.
Thank you for your understanding.