Last night I did an update and reboot. After that, I couldn't reliably play any flash videos. They would either go too fast or stutter (as if they were buffering every 2 seconds). This occurs in both Firefox and Chrome, however I'll troubleshoot in Chrome because it's easier to enable/disable plugins at will.

With PPAPI enabled (and npapi disabled), flash videos play at 1.5x speeds and audio is scrambled.

With NPAPI enabled (and ppapi disabled), flash videos stutter and skip, despite showing a decent buffer.

From one old thread, I went into pavucontrol and tried disabling the high def audio controller. I also tried disabling Totem plugin to no affect.

Version other details:

Linux freshdesk 3.2.0-29-generic #46-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
$ cat /etc/*-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04.1 LTS"

Shockwave Flash 11.3 r31
/opt/google/chrome/PepperFlash/libpepflashplayer.so
11.3.31.331  PPAPI (out-of-process)

Shockwave Flash
Version:    11.2 r202
Location:   /usr/lib/adobe-flashplugin/libflashplayer.so
Type:   NPAP

01:00.0 VGA compatible controller: NVIDIA Corporation GT218 [GeForce 8400 GS] (rev a2)
01:00.1 Audio device: NVIDIA Corporation High Definition Audio Controller (rev a1)