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I have tried

F12:: Send, {LAlt Down}{=}{LAlt Up}

which was recored by Macro creator but did not work. Also a variety of changes like !{=} , !=, and SendPlay as well.
It seems it is not possible to remap Alt + = in Onenote using Autohotkey. However, those with Ctrl shortcut can be mapped with Autohotkey though.
Do you have a solution ?

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Both F12:: Send {LAlt Down}{=}{LAlt Up} and F12:: Send != worked equally well for me. After you added the mapping to your script file did you tell autohotkey to reload it? – Glenn Stevens Jan 31 '13 at 7:48
Did you try it in Onenote ? The problem is somehow it is not possible to remap Alt shortcut in Onenote application. – user1502776 Jan 31 '13 at 16:54
Yes, @user1502776 I tested it in Onenote (Onenote 2010) and it worked fine. If I hit F12 it opened up the equation editor. – Glenn Stevens Jan 31 '13 at 19:19
I don't understand but it works now. Really strange indeed. Thanks Glenn! – user1502776 Feb 1 '13 at 0:29
up vote 0 down vote accepted

Here is the working code that I use and I few others. Please feel free to change the F-shortcut to fit your habits:

#IfWinActive, ahk_class Framework::CFrame
;Insert Math equation
Send, {LAlt Down}{=}{LAlt Up}

;Insert boxed table
Send, !nt{Right}{Enter}{Right}

;Make table borderless
Send, !jh

;Bring up Table Layout tab
Send, !j

;Bringup Math menu
Send, !j
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