Hi James,
Yes I would expect that the printed result would match the preview screen. This is because Previewing a cheque uses the same printer driver and all the same options.
If you are confident that the printer driver is not the cause of the differences in print-out alignment, then something else has to be different between the Win98 machine that can print cheques successfully and the machine(s) that have a margin problem. Identical machines with identical setups cannot have differing results. You will have to go into things such as how Windows is setup (ie screen resolution, large fonts, DPI settings, etc). You might also want to verify that the problem is repeatable on different cheque specifications, not just on this specific one.
This is starting to become something that is difficult to answer over a support forum. You will probably need someone to visit you on-site to investigate what is different between the workstations. The consultant who sold and installed Adagio Payables for you would be a good first choice on who to contact.