I recently took a four shot vertical panorama of a lighthouse and obtained my best results in Photomerge Cylindrical after rotating and saving each picture counterclockwise. This has worked well for me on other vertically challenged pano shots as well

If you want to test other software here are some links:
Autopano Pro from http://www.autopano.net
PTGui from http://www.ptgui.com
Open source software Hugin from http://panospace.wordpress.com/downloads/#devel

And here is a list for panorama related software for various platforms: http://wiki.panotools.org/SiteMap#Software

I wonder if you can post the result (not a too small version), because cylindrical projection is unsuitable for vertical panos of buildings, etc., for it has a "curving" effect. If the total angle of view is too much for rectilinear projection, there are other option, though Photoshop is not among the decent pano stitchers. Panorama Tools Assembler is the best value, a full-blown professional stitcher for the least money; see http://www.tawbaware.com/ptasmblr.htm (Hugin is free, but with limitations).

True, but it probably doesn't show for a lighthouse.

Cheers,
Bernard