Are you printing checks with a laser printer or a dot-matrix printer?
What is the layout of your check - check/advice or advice/advice/check, etc?
Can I confirm that the advice section on your check is printing as expected, both in terms of size and position? And that it's only the check section that is vertically mis-aligned by 5/8"?
If indeed the advice is a laser form and perfect, and only the check is vertically off (not horizontally), then we can probably rule out a system/printer driver situation and focus on the check specification. You can print the check from the designer (to plain paper) to test print alignment without using up check stock.
If the check comes after the advice, it may be that the height of the advice footer section is too big (or too small) by 5/8". Or whichever section happens to be immediately before the check.
Also determine if there are any fields hiding underneath the check section title bar. Left-click on the grey 'Check' section title and use the up/down cursor key to move it a bit. If there is any fields hidden, delete them. Then move the section title bar back in the same way.
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Regards,
Softrak Tech Support