I was experiencing this issue as well, but was able to resolve it after speaking with QuickBook's online chat tech support. Here's what we learned:

-- If you're using a web browser like Chrome, try switching to another like Firefox.

-- Check if it works OK in Firefox, and if it does, it means you need to clear your COOKIES in Chrome.

-- Even when we tried an Incognito/Private window in Chrome, it didn't work until we cleared the cookies.

After following these steps my transactions are auto-matching again. Hope this helps others having the issue!