Mouse hesitation in 3D games (Starcraft 2, TF2)

Hello all,
I'm currently running an older Mac Pro (second revision I believe) with an upgraded video card: ATI 3850. I have 7GB's of quality memory and have the system connected using an MX518 mouse.
I had to patch to 10.6.3 in order to run Starcraft 2 successfully (it seemed anyways, it didn't want to run earlier and I read reports that updating the OS helped them out). Well, it got my game running but it's causing an issue (That I thought until recently was Starcraft 2 related).
After leaving the game on the menu screen for more than a few minutes, my mouse starts to hesitate when moving it across the screen. It moves for a moment then pauses, and then continues from where it was. It's literally pausing for a moment. I can bring a browser up and other software and it's affecting the entire OS when SC2 is running. I can enter a game and have no problems - sometimes however in the middle of a game (sometimes after as few as 5-10 minutes) it can start doing this again.
I had thought this was SC2 related, but then when loading up the now available Team Fortress 2 from Steam/Valve - I am seeing it having the same issue. The difference however is that in TF2 I can command tab out to the OS and things run fine.
It's almost as if the games are dragging my system / bus speeds down .. like there's some kind of graphic memory leak or something but I'm not sure where to go with it.
As an aside, I've loaded 10.6.3 on my Mac Book Pro and left SC2's menu screen up for an hour with no problems - so it's defintetly my Mac Pro.
Any idea where to look? I'm about to - for the first time in 3 years wipe my drive and re-load the OS to see if it cures it but figured I'd try here first.
Thanks,
Adam.

Hi,
I've just been through an Apple Care experience for what I believe is the exact same problem. I am running an ATI HD3870 PC&Mac edition on 10.6.4 with Steermouse and a Logitech G9x mouse. I was seeing the problem occasionally in World of Warcraft, but was able to reproduce the issue reliably within StarCraft 2.
I believe that I found the root cause of the mouse issue through the diagnosis procedure the Apple Care representative took me through. To reproduce the issue I would run through the tutorials in order and by the time I would get to the 7th or 8th tutorial the mouse would begin stuttering.
I did a fresh Snow Leopard install from the DVD to a spare partition and ran through the reproduction sequence twice. Both times, at the usual place where the issue would present itself, the screen blanked out. Immediately I recognised this as the graphics card protecting itself most likely due to overheating. It seems to me that the drivers in a software update (no idea which) to 10.6 are preventing the card from entering this protective state (I think ATI call this VPU Recovery Mode under Windows).
After seeing the base Snow Leopard behaviour I took the vacuum cleaner to the machine, scraped some very dense dust from the heatsink on the card and installed SMCFancontrol2. I have set the minimum fan speeds to just under 1k rpm. Also, there are reports that StarCraft 2 is not frame limiting on the menus or interactive 'areas' (bar, bridge, armory etc). I entered the recommended lines into the Variables.txt file (frameratecap=60 and frameratecapGlue=30) which will limit the load StarCraft 2 puts on the graphics hardware during these scenes.
I am now unable to reproduce the mouse stuttering issue. The tier 2 support representative to which I spoke this morning wasn't very helpful. He didn't want to accept any of my findings and denied that there are any issues with the drivers. I asked him to escalate my findings upward but I doubt anything will come of this.

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    17 * * * Request timed out.
    18 * * * Request timed out.
    19 * * * Request timed out.
    20 * * * Request timed out.
    21 * * * Request timed out.
    22 * * * Request timed out.
    23 * * * Request timed out.
    24 * * * Request timed out.
    25 * * * Request timed out.
    26 * * * Request timed out.
    27 * * * Request timed out.
    28 * * * Request timed out.
    29 * * * Request timed out.
    30 * * * Request timed out.
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