Yes you're going to have to modify the files under your themes webAppIntegrator folder to get the same look and feel as your custom theme.
Depending on your theme implementation you may be able to accomplish this with only CSS changes but your theme developer should know.

The webAppIntegratorBanner.jspf file contains the code that starts the processing of the launch menu





Ryan

SCJP & SCWCD
IBM Certified Solution Developer -- WebSphere Portal V5.1, v6.0

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