RE: Reference and comment field on invoice
They are showing for me. I am using the default 80 column layout though. In that layout it is directly below the shipping address of the customer.
Have you installed any addons possibly that changes the layout?
Also check the layout, do this by exporting the layout and opening in notepad. Search for "Reference:|" Transaction.ReferenceNumber
if you don't have that on the layout, then it would need to be added.
Also please note, that if the comment is blank on the default layout, then the system will not print the reference number. There is another post on the forum that details how to change the layout to fix that.