In InterWorx 4.8.0, there’s an important change that makes some custom themes look bad on two-column layouts (Web Server page, FTP Server page, etc).
The problem is that prior to 4.8, classes were used to address the main content window. This CSS rule applied a left-margin to provide space for the menu. A separate change to the two-column layouts meant that the rule now applies to the first column on those pages also.
The fix is to change the rule definition to use the id instead. In your theme.css, change anything that references:
.iw-yui #yui-main .yui-b
to the new version:
.iw-yui #iw-content
Then your theme will exude happiness and sunshine!
Tim