To be honest with you, I can’t re-create the problem that you are dealing with. I do agree with you however that it sounds like a simple set-up problem. Also, I have never used a Mac much less QuickBooks for Mac.
I do however have one suggestion. I believe that your problem would be solved and in the process your invoices would be more professional looking if you customized the invoice templates. Assuming that your Mac navigates similar to its windows counterpart here is what you do.
Click Invoices on the toolbar. On the top right of the invoice screen, you should have a drop down box with the name of your current template. Click it and select “Customize.”
On the dialog box that appears, select “Edit” then click on the “Header” tab. There you will find that you can change the wording of the field that show up on your invoice.
So now instead of numbering your invoices “Assessment XXXX” you can put the number “XXXX” in the “Assessment #” field. Then the auto numbering would no longer be a problem.
Since you probably use the invoices for special assessments, dues, member usage fees, etc. you would have to copy the template and change the fields on each to match what you are using it for (i.e. Dues #, User Fee#, etc.). I am sorry that I couldn't be more help...check back though as other users may have helpful solutions.