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I've not found any forum references to this, but it must be prevalent. I have tried three Linux boxes so far and on all can reproduce this issue. This does not occur in Windows.
When running any sketch in Presentation mode using P3D or OpenGL the first time the sketch is centered in the screen. The second time, and any time thereafter until Processing IDE is shutdown and restarted, it places the top left corner of the sketch in the center of the screen, resulting in the sketch being offset down and to the right. I can reproduce this easily. I can even take any sketch, such as the example clock (under Basics examples), add P3D (or OPENGL) to the size parameters and it starts behaving this way. Prior to making it a 3D sketch it can be restarted all day long and run multiple times without issue.
The real problem is with an exported application as it cannot stop and restart the Processing IDE and therefore requires a system reboot to restore the placement of the sketch window in the center of the screen.
Here's the PeasyCam demo run in presentation mode first time:
And here's the screen on subsequent runs of the exact same sketch in presentation mode:
What the heck is going on? I have an application that needs to run in Ubuntu in presentation mode and can't have the user rebooting everytime they run my application. Does anyone have a solution or work-around for this? Any help is very much appreciated.