Can you please provide the required information
1) Are you trying this on Office 2010 or some earlier version of Office(Please provide the Office version being used)
2) If possible, can you share the project for further investigation
I have the same issue using Adobe Presenter 8.01 in Win 7 on 64 bit machine in Powerpoint 2010. This bug exists for both MS Eq 3.0 and Mathtype 4.0. This bug has never been fixed. Does it occur because the equation is an embedded object? A lot more people in science might use the product if this worked.
Adobe presenter does not 'count' the animation, so it tallies one less animation than programmed for each embedded equation. The equations must be pasted as images to get it to work. This is unfortunate.
Could you please send your pptx file to firstname.lastname@example.org, I will investigate the issue that you are facing. Equations in general works fine in "Adobe Presenter 8" and it also honor certain animations.