I can confirm everything with my corrupted game.
I installed DebugEnabler and dumped the alarms. The XML generated from my game showed the same alarms for the TreeofProsperity. I then uninstalled the TreeofProsperity object with my game launcher. When I started the same corrupted game the lag and clock problems were gone.
Many thanks to everyone at Nrass, Cyron43, crinrct and everyone else who helped to solve this problem.
Does someone plan to report the TreeofProsperity problem to the EA bug team/store team?