We found a solution!

For those interested, the layout is just screwed up, obviously. We couldn't manipulate the Master in any way to automatically be correct when the layout is applied. The solution (see: workaround) that we came up with was to apply the layout to the slide, start creating it with the incorrect indents and bullets, then simply click the "Reset" button next to the "New Slide" button. This pushes the indents and bullets to the correct format based on the original Master slide.

I don't know why it doesn't just apply correctly the first time, but this fixed our problem.

Thanks,
Jordan