Check a couple of your files for the settings under Setup, Settings, Company, Forms to see if you have the checkbox set for Use Next Available Number.  I would suspect the problem company has it set but the others don't.

I don't see that specific checkbox in either company when following that path.

See the image below.  I haven't tested these options but comparing your files, you might be able to find the different.  It might be the Verify Number Sequence option too.

BTW, why don't you just keep the bottom stub from the cheque?

Interestingly, I do not have that column in either file.

Sorry, i didn't realise Pro and Premium do not have that setting.  The image I posted was from Quantum.

I just tested a Pro and Premium file and was able to print twice with the same cheque number using 2020.2 with the Pro Universl file.

I am not sure why you are having the issue.  The only thing I can think of is that there is something different with the Forms settings or you are using Premium in Multi-user mode and you hit Refresh Lists before printing a second time.

Otherwise, I would just start using the second stub as your copy or photo copy the cheques if you really need a copy of the cheque portion.

Hmmm, well thank you for trying

Yes, I do keep the third stub (in a sequential pile of all cheque stubs) and yes, I know that is probably un-needed duplication of information and that paper filing is going the way of the dinosaurs but this is the system I inherited and changing it is a much larger problem for another day!