I read somewhere that all tourist landing in Bangkok with a connection to another destination in Thailand are now required to pass throught immagration here. However if the airline that you are flying into Bangkok with has an agreement with Bangkok Air ( the only airline flying into Samui) then your bags can be checked straight through to there. Just remember that at the Samui airport go to the internationl baggage claim area and not the domestic one. You will clear your bags through customs here.
Maybe someone can confirm this as it is only the latter part of this year that these new rules became effective.
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