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I run Debian 5 + Gnome and it seems that after I made certain updates with aptitude, whenever I run a query in Navicat ( sql program that runs on WINE ), as the results are being presented linux goes into the command line and the GUI dies and it restarts and it asks me to login again ( all my programs crash ).

Has anyone experienced this before? Or does anyone have a clue as to how I could go about debugging this? I suspect it's some issue with Gnome and WINE, but I'm not sure.

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I'd try reinstalling wine. It could be some navicat configuration files stored in wine, navicat does seem particularly temperamental. Are you running the windows version under your own wine install or is it the one that's been packaged by them? If you need a fresh copy I could email one over.

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