I believe your source is incorrect: I verified the Alchemists guild by removing the apostrophe from the map file and it showed up just fine afterwards. Navigators guild doesn't have an apostrophe either, so it's consistent... On the other hand, Devil's Den for example does.
Interesting, this time both Troll Pit and Lost Vale of the Elders show up. Maybe there's another force afoot that makes my method of testing inaccurate? (Which was starting a game with about a dozen nations with 9 provinces each, then using F1 screen to compare the map-file and the game.) Well, who cares, with these corrections there shouldn't be any typo-induced flaws. Attached is a zip with both versions of the map-file fixed with the corrections. It's possible that I've introduced more errors to the mix so someone ought to double-check...
The scenario that has pre-set starting locations has room for 6 land nations only. Weren't we going to use that? It has two advantages: Firstly, it distributes players in a supposedly fair fashion. There are no nostart provinces at all set in the 'free'-version of the map, which might result in wonky placement. (In the extreme end, on the map there are a couple of nation specific sites that allow you to recruit troops there only if your capital is in the province in question. E.g. a house of Fiery Justice in #44. While impossible in the scenario, in the free version it's quite possible to start in #44 and thus gain the ability to recruit Grand Masters, even if you're not Marignon.) Huh, I don't really mind these balance-matters, so why am I the one doing the exposé? You choose!
Oh, be it as it may, I decided against Mictlan for another reason: in both maps there are a lot of possible extra sites in your capital. It would appear that the limit of 4 sites per province holds even in this case, so Mictlan with its three starting sites misses on the opportunity to benefit from the starting provinces that have two or more special sites. Thus I'll have Abysia, with only one special site, to maximize the possible boni to be had from starting placement! (Unless we go with the scenario in which case I'm stuck with R'lyeh, unless Stonebrow wants it. You should bug him into reporting for duty on the forum anyway
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