Ryan: The best way to make sure the chapter makers will be at the exact points you want them, is to place them before the MPEG-2 encoding stage. You're already doing that, because you set them in Final Cut Pro and then go to Compressor. Very well done, specially for someone who says is not familiar with DVD Authoring. Many users have no clue about how to turn regular FCP markers into chapter markers, and how to include them in the exported master. BTW, setting them in Compressor's mini timeline would do it too (without the flexibitility of FCP's timeline, of course).
Since you did everything well, the suspect is... Windows Media Player itself. It's not really reliable as a DVD player. Nothing you can do about it, then
You could try other Windows software DVD players, like PowerDVD, and see if they behave. It's something.
Hope this helps.
Adolfo Rozenfeld
Buenos Aires - Argentina
www.adolforozenfeld.com