Automatch is borking my Cheque numbers.

I went to enter a new cheque using spend money. But on save, I find it wont save, because the Reference number is alread in use.  

I go looking for the reference number (a unique cheque number), only to find it has somehow been allocated by Essentials to a bank feed transaction when it made an automatic match based on my Alocation Rules.

It this expected behaviour?  Have I been doing something wrong when entering cheques with Spend Money, by filling the "Reference number:" box with the Cheque #?

Is the correct process to leave the  "Reference number:" blank to allow MYOB to enter a SM000XXX sequence and enter the Cheque # in notes field perhpas?