I am having this same issue. My bank has a check number as a text link but I only use a check once a month for my water bill. However I believe that Quicken online is looking at the first, say, 20 lines of the account database and building it's records off that. When it scans that at first and doesn't see anything in the check number column it simply discards it and moves everything else over when a check number is there. This is a huge problem and I contacted support almost 6 moths ago with no response. It makes everything waaaay off and makes the program usable.
  I will send them more support tickets and see if we can get this resolved. Knowing what i know about programming, they should be able to go in and override the number of forced column reads and grab the check number column regardless of whether anything is there or not, thus making sure it places the correct info into the correct space in their system.
  I have attached an example of 2 such transactions that force everything else to be off by a large amount.