I will enable the log and post some results for you next time we hook up for a game, probably Saturday.Seven05, do you have your civ set up to make a Python debug log? There are some print statements in the findStartingPlot function that might indicate whether it's being recalled after the initial placement. If it's re-calling the default procedure in the DLL though, nothing would show up.
As for the floodplains, I've had to modify it for myself (three types of desert in my mod). From a gameplay standpoint I think the only case outside of deserts that makes sense would be tundra since tundra is about as useless as desert unless you're lucky enough to have some trees. If you place them on plains/grassland they quickly overpower the normal food resources, or worse yet- they make cottage spam even more potent.
Anyway, I think as a 'pure' mapscript you should avoid any fundamental gameplay changes.