I think this might require some hands on, since it sounds like an issue with your specific application. You might reach out to your Pega contacts to see if there's anyone on our services team who might be able to assist you. I can give you some general pointers though.

When looking at something that doesn't match, I first want to determine if the issue is that something has changed, or if there is something else going on.

1. If you are on a page and something you expect to match is not matching, interrogate the control again and compare the match rules for the new one to the old one. Perhaps there is some difference that you are not noticing right away.
2. Try Selecting the control in Object Explorer and Clicking the Refresh Matching button (the orange one) and see if the control matches. You might need to call that at Runtime in that case, although I would be careful here and try to determine why you need to call it as this isn't very convenient.
3. If the issue only happens at Runtime, perhaps you are using a different account than what you are using in Interrogation and that explains why. If not, then you might also be going to fast. Another potential issue might be ambiguous matching. This occurs when you have match rules that are too lenient and allow controls to attach to each other. If you have a control you've interrogated first that has lenient match rules, your new control might get matched by the first one which would explain why at Runtime you see it as not matching.