Which version of mac os x are you using?
I don't think it should make any difference, but are you running cs5 in 64 or 32 bit mode?
Does using one mode or the other make any difference?
If you go to /Applications/Adobe Photoshop CS5/Presets/Scripts, do you see a Photomerge.jsx and a Stack Scripts Only folder?
At the bottom of the File>Automate menu does it say Show All Menu Items?
Could you post a screenshot of the File>Automate menu in photoshop cs5?