Sorry for resurrecting such an old thread, but the problem does not appear to have been solved and I am experiencing the exact same thing. The browser continues to run normally after the game freezes. I'm using Arch Linux with 64 bit Flash 11.2.202.418. The game has run just fine up until this point.
--edit--
Also just noticed that this thread lives in the Machinarium on Linux portion of the forum. Perhaps a mod should move it to Samorost 1 and Samorost 2?
First off, thanks for pointing out how this Samorost2 specific question was left in the Machinarium on Linux board.
Re: your freeze, have you tried the advice that ABoretz suggested regarding the use of a 32-bit compatibility package? I know bupkis about Linux, but I DO know that Samorost2 was originally built on 32 bit system software. Perhaps that's what will be needed on your end... ?
Lastly, neither Croconux nor e3k ever wrote back to let us know if they ever solved their freezes. Please DO follow up when you find a solution to your problem. It would be much appreciated if you could. ~A