It seems to happen at random.
Like the Dual Core Timing Issue but cpus=1 kernel flag does not fix it.
As well the duel core fix on the iPC 10.5.6 PPF5 does not help.
Mouse pointer lags when you move the mouse. Also the pointer likes to skip around the screen.
If I do manage to get the mouse to the dock I noticed that the dock animation is also slow.

This is after I have a fully working system QE & CI enabled.
I installed a zephroth patched itunes 8.02 installer and after restart I got the lag.
But when I booted over to my text OS X install on another drive it too had the lag.

Once I installed paragon ntfs and that gave me mouse lag after reboot but I removed the applications folder and that fixed it.
Another time I installed parallels and after reboot it had mouse lag.

Some help would be appreciated!

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Rig: Home Brewed OSs: Vista SP1 & 10.5.0 Retail updated to 10.5.7
CPU: Intel E8400 Core 2 Duo
Ram: OCZ Reaper HPC Edition 4GB (2 x 2GB) DDR2 800
Mobo: Gigabyte EP45-UD3R
Graphics: 8800GT 512MB- CI/QE Full Res enabled with NVkush
Wireless: Motorola WPC1810G Detected as Airport OTB
Onboad Audio:
HDD: HITACHI Deskstar P7K500 500GB SATA + 400GB SATA + 74gb SATA Raptor
DVD: Pioneer DVD-RW DVR-116D IDE + Lite-On DH401S SATA Blu-Ray drive