I've been having the same issue over the past few months. Normally, downloaded transactions show up in the register with the little green box and the C above it in the reconciliation status field. I'm an accountant user with several clients in QBO and I always use an incognito Chrome browser when I'm logged in. Recently, for multiple clients, the green box is there for downloaded transactions but the C is not. It is not 100% consistent in that sometimes the C is there but it almost appears that this is happening in batches where a small timeframe will include the C and another small timeframe will be blank but all have the green box. I've been either waiting until month-end to reconcile these to correct for this or manually changing each transaction to a C but it is time consuming to continue to do this. Is there some kind of glitch happening on the back end? This is becoming a consistent issue for me and since it is happening in more than one QBO account, it doesn't appear to be an isolated problem.