Also having this issue with our last payroll of February.  I partially resolved it by going to the register and clicking on one employee with the problem and selecting edit, which brought up the payroll history of all.  I then went to "edit paychecks" and one by one deleted and re-entered the check numbers.  It worked on all but the last one I did (4/5 employees).   There are so many glitches and issues with QBO it's ridiculous for the amount we pay.