@TehSDragon:
According to Hox's website, some of the shorter chapters collected in the Tankobon were merged into one longer chapter, so the chapter numbering is all messed up.
You'll notice that some of the chapters here have a volume number on them, and others don't. The ones without a volume number are from the magazine, and thus use the alternate numbering.
Looking on Hox's website, ch 97 in the magazine is The King's Left Hand (3): http://hoxtranslations.blogspot.com/search?q=historie+c97
So, you're not missing anything story-wise by switching to the magazine numbering... However, the art is usually touched-up for the tankobon release, so it might be better to wait for that reason.