Site Down Settings Problem

[earcandy]

Ive been using site down to develop my site. I have completed it and disabled site down, however the site looks completely different because the gallery doesn't appear even though its enabled (it does appear if I reactivate site down) and the search box appears even though its disabled (it does not appear when viewing the site when site down is reenabled.

I have cleared the cache with no change.

Help!

[staartmees]

please post system info and perhaps the url