Another update:

After I posted my concerns here, I did also call the hotel that I frequent at, where the shortage of eligible amount occurred.

Today, I got a call from the front desk manager and he said, after investigation, it appears the short is caused by my Diamond breakfast?! This Regency doesn't have lounge, so the Diamond breakfast happens in the restaurant. I would bill against the room and they would remove the charge. From what he told me, all Diamond related perks will short your eligible base amount? This just doesn't sound right, as it seems to penalize Diamond members!

I am questioning this explanation because the shorted amount is never the same. Suppose the Diamond breakfast does reduce earning, then why is the shorted amount vary, even from the same hotel? I had similar miscalculated base point issues at other Hyatts with RC... so i don't entirely believe this explanation.

This is becoming an increasingly mysterious problem.