The max frame rate setting in AH (45 or 60 or unlimited) doesn't actually change anything related to the refresh rate of your monitor (it just limits how many extra frames AH tries to render).
When you play a game in full screen mode that has different resolution from your normal Windows screen, the montior switches to that mode. Often you haven't used that other mode for Windows and so you haven't set the refresh rate for that mode. Set your desktop temporarily for that mode and then use Settings, Control Panel, Display, Settings, Advanced, Adapter, and then select the refresh rate you want in the box at the bottom. Then, when AH uses that resolution it will also use that refresh rate.
(These instructions are for Win98 but the idea is the same.)