Looks like the subjugation treaty was the cause of the problem (at least in my instance).
First I tried scrapping research facilities, and I scrapped them all the way down until the score screen was showing 47.6K RP's. The research screen was still holding steady at 50K.
Reloaded the original save, and broke the subjugation treaty with the neutrals. My RP's were correct the next turn at 67.1K on both the research screen and the score screen.
Assuming that RP's are "paid" as tariffs by subjugated/protectorate empires (though the Treaties screen doesn't reflect this), I suppose the bug is related in some way to this.
Edit, after more playing: Ok, confirmed: Forging a subjugation or protectorate alliance with a neutral empire (possibly any empire for that matter) when your RP's are above 50K causes your RP's to DROP to 50K and remain there until the treaty is terminated. I can re-create the bug every which way from sunday. I'm sending the savegame and my analysis to MM for fixing. Yucky bug, that. You have been warned
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Do any of you guys who had this problem remember if you had a subjugation or protectorate treaty with any empires in your games?
[This message has been edited by Voidhawk (edited 01 January 2001).]