Found this topic by googleing my similar problem, not sure it is fully related to the problem of the topic opener, if not then I apologize...
I have a similar problem upgranding from 1.1.x to 2.0.1 except that I have a dual monitor system and the lag happens only if the VLC window (fully or partially) resides on my secondary monitor. It uses 100% CPU (on one core) and skips frames if the VLC window size is large enough or in fullscreen mode. The CPU usage depends on the size of VLC window, if I start to resize the window to bigger and bigger then the CPU usage gets higher and when it reaches a certain point then it starts to drop frames. It does not seem to depend on file formats.
There's no problem if the window is only on the primary monitor, not even in fullscreen mode.
Here's the messages :
http://pastebin.com/rraV64RP , this is with default VLC settings.
System:
WinXP SP3 x86, Ati Radeon HD 4350, two indentical 19" LCD both connected on DVI
To make sure it's not a driver issue I upgraded to the latest Catalyst video driver package avaliable from AMD.
Now I am also downgraded to 1.1.11 until this gets fixed, but those who do the same be aware that the last available VLC windows build is not secure so you'd better remove a few plugin dll's (
http://www.videolan.org/security/) as there's no higher 1.x builds than 1.1.11 for Windows that fixes these vulns... (btw. any reason why isn't so?)