Congratulations!
It may have nothing to do with the space between, but only the one or two markers that were in a position for it to matter for this particular layer break.
I agree with John; don't let Encore transcode an already compressed mpeg export.
The preferred method is to export from Premiere/AME as MPEG2-DVD so that Encore does not transcode it again. (Chapters need to be created in Premeire.) Use a bitrate calculator to find the datarate, remembering to allow for menus, especially motion mens, audio, etc.
A workaround is to do what you are doing, then examine the Encore transcoded file and see what the datarate is. The export it (again) from PR, at those rates. Use Replace Asset in Encore; make sure the new file has a different filename.