Updated: December 8, 2012
The problem you may be facing is as follows: after upgrading to Flash Player 11.3 or higher, you may be seeing choppy playback in Flash movies on some websites, under some situations. For example, Youtube movies might be all smooth and dandy when viewed on the organic website, however embedded instances might not.
I was faced with this same issue recently, on Windows. The problem would occur with Firefox while watching embedded Flash videos, however Chrome was not affected, most likely because it comes with its own version. While playing embedded clips, the video would turn slow and jerky on any mouse motion. Moreover, dragging the mouse cursor through the embedded player space would cause it to stall and jump about. So how do you go about resolving something like this?
A word of caution
Now, before we begin, let's reset the disappointment meter. It is impossible to fix all and every Flash-related problem in a single article. It is also entirely likely that you will stumble upon this tutorial through a Web search, believing it may help you get your Flash performance to its smooth normal. Your woes may be completely different and completely unrelated, so please be aware of the chance, however slight, remote or real, that this tutorial might not help you, at all.
Flash Player performance
If you're seeing a choppy playback in embedded videos but not organic ones, this probably means there's something in the Flash Player that restricts the playback of embedded content, probably because it points to third-party sites. So a word comes to mind, security.
After seeing the phenomenon affect my box, I realized there might be a new feature in Flash Player 11.3, which may not have been existed or may not have been activated before, which is causing the performance problems.
So, some research is needed.
Research
Reading through the rather rich Adobe knowledge base, I learned that Flash player 11.3 comes with its own self-sandboxing mechanism, known as the Protected Mode, designed to limit the impact of attack launched from malicious SWF files. The addition of this feature is probably necessary due to the vast amount of exploits targeting the Flash Player, but we will get there.
Anyhow, reading from an article labeled How do I troubleshoot Flash Player's Protected Mode in Firefox, I discovered that the Protected Mode can be disabled, even if it's for the sake of temporary troubleshooting. Now, a word of advice and warning sort of, before we proceed: Do not attempt this if you're worried about your security and if you think the world might crash on your shoulders. The reality is a little less grim, but more soon.
How to disable the Protected Mode
So, what you need to do is navigate to the relevant Flash folder and edit the mms.cfg configuration file. The relevant locations are, for 32-bit and 64-bit Windows 7, respectively:
C:\windows\system32\macromed\flash
C:\windows\syswow64\macromed\flash
The file cannot be edited inline due to write permission restrictions, even if you launch the Windows Explorer with administrative privileges, so you will need to copy a file somewhere else, open it, and then add or edit the following directive:
ProtectedMode=0
Something like the following image:
After this is done, copy the file back to its original location. Please make sure that the configuration file is safely backed up before making any changes, especially if you're less savvy about this kind of tweaking.
Next, restart the browser and test. If this works, fine, you're done!
Security, the CORRECT way
Now before you all naysayers accuse me of offering an easy way to clueless users to compromise their operating system security, let's recap what we have done here and introduce a superior alternative.
First, if a security measure causes a negative impact to the user, be it the loss of performance, responsiveness, smoothness, stability, features, or anything else, then the security measure is useless. The security must complement normal usage patters and not replace them. The security must be seamless and transparent.
To that end, the Protected Mode might be welcome, but if the user is tempted to disable it, so they can watch videos, what the Flash Player has been designed for in the first place, then there's no meaning to the protection. And let's put hype and politics aside.
Instead, you can use something like EMET, a zero-impact technology from Microsoft, to harden all your externally facing programs, including browsers and the Flash Player and gain the same, if not better security level, without any compromise on quality.
Conclusion
This article may be focused on trying to resolve one of many possible reasons for slow and choppy playback of videos, embedded or not, in Flash Player, most likely version 11.3, used in Firefox. But it ends with a much more important message, if you care to read.
Hopefully, you are now a little more familiar with the Flash Player settings and internals, you know your way around, including the useful forum discussions and FAQ, you are more versed in searching and defining your problems and finding the correct solutions, and most importantly, you understand that decent security can be achieved without any loss of functionality. And that's the whole point, regardless of what software you use.
Well, I guess that would be. Happy watching!
Cheers.