The wheels turn very slowly at Quickbooks it would appear. I have been putting up with this same issue for close to a year now. Today, I decided to look into the cause and came across this thread. The exact same 'solution' works for me to:

1. The rules are identifying my transactions and you can see which ones have the 'Rule' text against the transaction, however, they are not being automatically added even though this feature is turned on.

2. If you then go to edit any rule but don't actually make any changes and simply save it, all the rules run and the bank feed is cleaned up.

This is quite obviously a software bug. I'm surprised it's been logged months ago and still not resolved. I guess this is why Xero is the market leader. May need to look into a migration to Xero and just pay the extra money for something that works.