Sounds similar to the issue that occurred with ebates. The stores are struggling to stay afloat (look how many closings have been mentioned lately.) When it comes time to pay the bills - affiliates/reward sites are at the bottom of the list. If the store does not pay the reward site, most will not eat the loss. Therefore, they do not pay you. I think it at a point where it is a gift. If the reward comes through, good for you. I would not count on 100% payouts anymore.
As for the bonuses - that is just bad business. But, my guess is the bonus money is part of the "profit" that MyPoints makes. So, if they didn't get paid - they won't pay you.
I think you are spot on tracking your purchases and keeping your receipts. I would inquire again on the 14 day point. And, I would start questioning right at the window they give for credits. (I don't shop there - is it 30 days?) And don't forget - if you do not receive satisfaction - there are a lot of other reward shopping sites.