We're having similar issues.  We're trying to find someone at Intuit that can provide us with a copy of the cancelled check to show when/where/who deposited it since they are telling us it was deposited but our vendor states they didn't receive it.

Other check payments aren't marked as "paid" yet and are just marked as "shipped" but it's been several weeks and the vendors haven't received them.  We're going to attempt once again to get someone on support/chat that can help to void/stop pay on Intuit's side and then we'll hope to get the $ back in our account.  We did receive refunds on 4 checks that the vendors never received and we had used support/chat to void/stop pay but it took several weeks.