I am testing now:
- Phoca Cart template (the one you are using - version 1.0.4)
- with different size of boxes (one box has longer name of category - the same like on your site)
and everything is OK with the boxes, see image:

So really hard to say what can cause the conflict


Do you use some cache or similar feature, which can somehow display not updated site when chaning the equal height parameter, etc.

Jan