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When playing those mini-game puzzles, gameplay is slowing down after a while.
This doesn't happen when roaming the areas, only in puzzles.

Any idea how can I solve this?
I noticed that Machinarium is flash made. Maybe changing some flash options make it go smooth...

Any ideas?
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Try disabling hardware acceleration in Flash settings.
You can also try to execute the game directly with the Flash interpreter, but you need to chop the first 4432896 bytes of the .exe file to have a clean .swf file.
what do you mean, "slowing down" ?
can you describe it more detailed