I'm having this problem using Mathematica. I did find a work around. If you use the -noSplashScreen option wnck-applet doesn't spin out of control. I can consistently reproduce this with Mathematica. I'm sure you can duplicate it with the free trial version of Mathematica. -- wnck-applet consumes all cpu when using motif applications https://launchpad.net/malone/bugs/36928
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