Maybe a driver issue then...?
I don't mean to sound like a fan boy,
but I bet you wouldn't have these troubles with a GeForce...
Maybe it's just failing to treat PCSX2 as a "High Performance" application (possibly on occasion)...?
Or worst case scenario--
You got a bit faulty unit.
I don't know the details of your PC games (exact performance, settings, relative compatibility, etc...),
but I wouldn't be surprised if it shows more with a very performance sensitive application such as PCSX2.
Especially if you have "exactly the same everything else" with PCSX2.
I don't mean to sound like a fan boy,
but I bet you wouldn't have these troubles with a GeForce...
Maybe it's just failing to treat PCSX2 as a "High Performance" application (possibly on occasion)...?
Or worst case scenario--
You got a bit faulty unit.
I don't know the details of your PC games (exact performance, settings, relative compatibility, etc...),
but I wouldn't be surprised if it shows more with a very performance sensitive application such as PCSX2.
Especially if you have "exactly the same everything else" with PCSX2.