Hi all,
I acquired Machinarium in Humble Indie Bundle 3 and had the reported difficulties with mouse movement and menu selection, making the game unplayable. So I removed Flash 32-bit and installed version 11 beta 2 64-bit from Adobe site - just extracted the files from the tarball and did
cp libflashplayer.so /usr/lib64/browser-plugins
as per openSUSE forum How-To, and it works nicely in windowed mode (hardware acceleration, mouse, etc), but fullscreen is still a problem.
Last I checked, Machinarium ships with its own version of Flash (10.0). It's a very old version, and 10.3+ (especially 11 beta 2) have come a long way on Linux. So no matter what version of Flash you have installed on the system, the game still uses Flash 10.0; the version it ships with.
You can check this by right-clicking in the game and going to About Flash Player.