Hi,
I've run into this a number of times. The frustrating thing is that Simply tells you it's going to use the next cheque number (and there's no way to stop it or change your mind, other than pulling the cheques out and putting blank paper in.) Unless you put in the cheque it wants before you click OK, you now have wasted two cheque numbers.
I use a period - i.e 100363. looks OK when printed out.
To find out why this has happened, look at the cheque log under Reports | Banking. If you are in the process of preparing a cheque and lose connection to the network, the power goes off, etc. after you print, but before you post, the program may flag the cheque as used, even if it was not.
I've also tried correcting cheque numbers after the bank records the number on the statement based on the MICR encoding. That can confuse the program too.
I hope that helps,
Randy