MOBI in general I'm afraid. All of the applications which convert HTML to MOBI simply have to translate HTML+CSS into ancient HTML plus a few proprietary HTML tags - no CSS at all inside a MOBI file. That's one of the reasons some CSS seems to work and some doesn't - if it can't be translated into fairly simple HTML (think 3.2, and not even all of that) then it most likely won't be retained when the file is converted into MOBI format.
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