Testing two builds with the new OS X cross-compiler showed that browser/omni.ja differed. More exactly, only the contents of chrome.manifest showed some reordering.
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I investigated the omni.ja packaging step and nothing jumped out at me that could explain the diff in the omnidiff attachment. Thus, I run 20 package tests on Linux and 20 on Mac and they produced always the same omni.ja. My new idea is that the step generating the browser.manifest which in turn gets merged into the problematic chrome.manifest during omni.ja packaging is the culprit here. Looking into that now.
Okay. Just rebuilding the browser part does already trigger the problem. This takes much less than a minute and I can start debugging this seriously. The other option that is helping us is building with -j1 (according to Mike Hommey) which I'd avoid if I could.