I would shoot the GM a letter describing the events that took place during your stay. Even a link to this forum thread would be helpful to them.

Credit card chargebacks usually can be processed within two business days. The time that it takes to post to a user's credit card account varies depending on the financial institution.

Marriott Reward points are typically only calculated on the dollar amount spent (room rate), unless a certain promotional code is used. If adjustments have been made in the past at this particular location, it may be that they set an incorrect precedent and are having some consistency issues in following through on it. In my experience (15+ years) as a GM, There are very few times when adjustments need to be sent in manually for MRWD points. It does take up to three weeks to process these points that are sent in manually, especially if the property is sending a fax and not entering the information directly to the Marriott Rewards Service desk.

As a GM, I would want to know the inconveniences that you described. You have given the right channels ample time to correct the errors you encountered. I hope this helps.