mkvmerge causes stutter when skipping chapters

I've been experimenting with MakeMKV and I am very impressed. As a comparison, I used a source DVD to create two MKV's, one using MakeMKV and one using mkvmerge. I compared them with VLC and interestingly, I found that when I skip chapters in VLC (shift+N), the MakeMKV file behaves like a champ, advancing to the next chapter as fast as I can use the keyboard. When I do the same thing with the mkvmerge file, there is a significant pause before the playback advances. I haven't timed it, but it can be as long as several seconds and it happens every time I skip by chapter. The mkvmerge file is never as snappy as the MakeMKV file.

To test it further, I demuxed and re-merged the MakeMKV file using mkvextract and mkvmerge, and the same thing happened; the file would pause before jumping ahead. I checked my hard-drive thinking it might be fragmented, but it was clean (I defragged anyway, though), and I made a copy of the original MakeMKV file just to help confirm the difference was with the files (I had several test MKV's from mkvmerge, but only one from MakeMKV). The copied MakeMKV file behaved exactly like the original.

As much as I like MakeMKV, I'm still going to need to use mkvmerge to touch up the files after MakeMKV is through. I'd appreciate some help figuring out why mkvmerge is doing this, and hopefully, in finding a way to fix it. Thanks!

Software:

WinXP SP3
MakeMKV 1.8.4
mkvtoolnix 6.3.0
MKVExtract 2.2.2.9
VLC 2.0.5