Well, in fact a couple of days ago I installed a vanilla SH3 onto my computer to see whether it's a GWX problem. I experienced the same "moon reset" issue in the stock game, so I think it has nothing to do with GWX. If it is really hard coded in SH3 than I am afraid we have to get along with it.
Anyway I still hope that the GWX dev team may overcome this problem. They worked wonder with GWX.