I am having the same issue with the botanist guild one.

Platform: Windows XP
ISP: Sunrise (Switzerland)
Connection: DSL
Time: 4/15/2011
Frequency: Always
Character: Pata Fihx
World: Trabia
Area: Gridania (3,3)
Class: All
Steps: A "!" shows in an unreachable area near the botanist guild in Gridania.

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As for the carpenter one, I think it might be the carpenter's r36 quest, where you indeed have to move to another area through a prompt menu. It worked for me (you are transported in another room in the back of the guild) but I did that one a few weeks ago, before the implementation of the first quests. Might be buggy now :\