QuickBooks Online copies the QuickBooks Desktop design for printing checks.
Here's the scoop:
Each bank account in QuickBooks keeps track of two check-numbering sequences: One for print stock and one for hand checks.
The assumption is that you'll print checks using printer check stock and hand write checks from a checkbook of standard checks (one you'd carry around) - where the two types of checks each have their own numbering sequence.
QuickBooks does not expect you to raid your printer for the next computer check and then hand write it. If you do that, then you're fighting the design - paddling up a creek without a paddle. 🙂
So, when you record checks "to print later", and then go to the batch printing feature, the check number that appears there should be the next check number from your computer check stock - incremented from the last check you printed. And, when you record a check with a check number, that number is your next standard 'hand written' check number.
It does appear that in the history of this thread, the hand check number on the check form was reportedly getting 'stuck' at a certain point, but that is no longer happening for me. If it was a bug it has been fixed.
And so...
If you record a new check, not "to print later" but with your next check number (from your hand checks), and pick Save and new as you record it, you should see the default check number on the new check increment by one. And, when you return to the batch-printing window, the check number there should be incremented by one from the last check you printed. If so, then QuickBooks is working as designed.