I was having the same issue many months ago and found this thread. Since it seems to be a known issue I have just been going to my list of many rules, selecting one (any rule), then hitting the edit button and update button (without actually changing the rule). Then my list of transactions would magically get entered via their auto rules. I was doing this daily for many months and then one day maybe a month or so ago, my rules started working without me messing around. I was beyond happy for this little piece of functionality to start working. And then it stopped working again in the last few days. The work around still works, but after having the rules work properly for a few weeks The work around seems even more tedious than it was before.
