I'm still having this problem of the Export dialogue box that disappears behind the CafeTran UI :(.
Confirmed and fixed in the coming build.
It looks like the Export button is the culprit: when I choose Export all documents from the Project menu, the Export dialogue box doesn't disappear.
Perhaps it's relevant: this hiding of the Export dialogue box happens when I click on the Export button above the project segments table.
I start CafeTran, I click the button Export, the dialogue box disappears. No other app switching involved.
Normally, the last steps that I execute before exporting, is running a bunch of QA checks. Perhaps that has something to do with it (with regards to losing focus or so).
To be able to confirm on my Mac, the issue needs to be reproduced. Here, the Export dialog appears in front right after clicking the Export button.