Whenever I make an instrument change inside my VDL template (e.g. from SnareLine (AutoRL) to SnareLine Manual), the Full Name Staff Margin changes so drastically that the first bar hangs off the left side of the page. I can make it look normal again by going to Layout>Document Setup and changing the Full Name Staff Margin from something like 14 or 28 to somewhere around 40, but it's a pain in the butt to have to do it every time. Any Idea what is making this happen?

P.S. It might be worth mentioning that sometimes I'm using customized versions of the instruments/drum-maps, but I've looked around and haven't found any settings that would seem to account for the margin change.

I'm also getting a similar problem when I add ossia staves (for cues or makeshift notehead keys) and when I edit the instrument names. The margin keeps automatically resetting to random numbers. I never had this problem before I started dealing with VDL instruments.

What you're describing isn't exclusive to the VDL template; it's a fail-safe built into Sibelius. As you get closer and closer to the margins defined in Document Setup, Sibelius will do what's necessary to keep staff related information within those margins. Trying creating a new score using a Film Orchestra or any of the other built in manuscripts. You'll be able to reproduce the same result if the combination of Page and Staff Margins take the staves too close to the edge of the usable space on the page. The staff margins will typically default to a margin large enough to fit all of the Instrument Names within the Page Margins. The VDL Template makes extensive use of tildas (~) to hide text in the Full Instrument names, so what you're experiencing might also be the result of those being included in the staff names.

I agree that it can be pesky at times, and it would be nice to have the option to turn this feature off.  However, it's not specific to the VDL template, and for the most part it keeps layout very clean around the margins. I would suggest going over to the Sibelius forum, make a detailed account of both your and Sibelius' behavior, and request that this feature be optional in the future, if you feel it's something that gets in the way of being able to work effectively.

However, what you're experiencing is something that only happens when you start encroaching on the page margins set in place.