Unfortunately, this is often unavoidable.
It may be possible to design to the smallest likely monitor size/resolution and use anchors to "scale up" some layouts, but not all. You can also mix and match windows zoom settings with the "enlarge window contents to improve visibility" setting you can select in FileMaker preferences on windows systems.
Ultimately, you may need to set up "preferences" table that uses the account or user name to look up the best settings for zoom and possibly even the ideal layout set for use with that user's hardware.
I'll look into building a preferences table (hope its not too far into my solution to implement). But what resolution do most of you develop for initially? I have a windows laptop user with 1600x900 resolution and another with 1366x768, a mac user etc. The 1600x900 is great because i can utilize so much screen real estate, however I'm thinking of creating 1024x768 to play it safe and not have the other users have to scroll up/down. Is there a rule of thumb that most devs follow?
No matter how you slice it, it's a major potential headache for Developing with Filemaker. The hardware manufacturers keep coming out with new screen sizes/resolutions--witness the recent release of a smaller format iPad.
Then consider how much screen real estate you gain if you provide support for working on two monitors instead of one...
A common feature request is that the zoom have more control than 25%, 50%, 75, 100, 150, 200, 300, 400
There are discussions about design on fmforums that focus on the subject.
Offering two resolutions of each Data Entry layout is the common concensus.