in Word 2003 vs. Word 2000 that should cause your problem if all settings are exactly the same. And yes, there are a number of settings that you must assure are the same if you are to get the same results.
You left out some specifics. You said one print-out was two pages longer than the other. Do you mean one was something like 3 pages and the other 5 pages, or one was something like 30 pages and the other 32 pages? This makes a big difference in trying to deduce potential causes.
You say the fonts and all four margins are identical; while in Page Setup did you also check that the Gutter settings, Paper size, Section start, and Vertical allignment settings are all the same?
Also you need to check everything else that affects vertical layout -- line spacing, spacing before and after paragraphs, pagination, etc. must be checked for all different paragraph styles used. Certain document-wide settings such as page breaks and section beeaks must also be the same.
If you have many different paragraph styles, the above checking can become somewhat tedious. Before checking everything in this way, I would lay corresponding pages of the two print-outs side by side and see exactly where the differences occur. If lines gradually shift, then line spacing is a prime suspect. If spacing between paragraphs is different, then look at the before and after settings. If paragraphs behave differently at the bottom of pages, suspect the pagination settings. You see the pattern of what to look for.
Because most, if not all, of the above settings information is carried in the Template used, make sure you are using identical templates. I don't mean just the same name -- templates can easily be modified so that a particular tempate on one machine may not be the same as the same template on another -- I mean are the templates truly identical?
What I might do is copy the Template being used on the ''original'' system to replace its equivalent on the ''new'' system (naturally, I would assure that the template being replaced is not destroyed -- I may want it back later). Are the print-outs now identical?
Hope this helps, and please let me know the results of your checks
Frank