Well, from what I see on your site, you didn't actually install J2.5 version of the template, did you? No wonder how things looks funny on your site. Install J2.5 version of the template
Give me a break...I did install the 2.5 template. You will see the template is V1.0 (of the J2.5 version presumably). Our J1.5 production site that we upgraded from is version 1.5.0 of the template. It has full version history starting from 1.0. There is no version history with the J2.5 template. According to the Rocket site, the latest version for J2.5 is V1.0 and for J1.5 it is 1.5.6.
It would help if there was some obvious identification on the template that identifies it as suiting J2.5. I mean, if you the expert couldn't tell the difference, what chance have I got?
Anyway, as you requested I installed the J2.5 template again to make absolutely sure (I don't even have a J1.5 install file) and it is the same one you looked at, except now the search box doesn't appear at all
First time around, I also downloaded and installed the J1.5 sources, but Rocket says they suit J2.5 as well (but the install file is named 1_5)