As michaelm said above
Go to
Then expand them. See whats listed at the flash player section - if you use Chrome and you have flash installed separately you should have 2 flash plugin instances there - the system's (installed by you) flash player that uses the old API and the flash plugin that comes with Chrome (uses the PEPPER API).
Disable the system's plugin and enable the PEPPER version. Restart Chrome then try again.
Is this a specific site problem or it happens on all sites?
PS there is a useful option in the advanced settings -> content (or what its called) named Click to play - this will make all plugins load only when you need them (you still have the option to run all plugins on a site if its done in flash entirely).