1. I am guessing, it marks as 'Overdue' up-until payment is applied to the invoice, as there is no specific due date for COD. You could simply turn off to not print overdue in Options.
2. Under Options, go to Invoice Layout -> Style. Scroll down to 'Text Block positioning'. See if you have logo selected there in one of the pull-down-list, and click 'OK'.
Hope this helps 