Here are the steps I've taken, and it has worked quite well:
1. Installed PCI-e USB 2.0 adapter card for the Virus TI.
2. Bought a power conditioner and am using that for the main studio gear connected to the computer and the computer itself.
3. Replaced standard IEC1363 strip sockets with surge protected ones, making sure to connect everything to the power conditioner so there's no possibility of ground loops. (Audio equipment is usually not grounded to Earth anyway, but may aswell make sure.)
4. Cleaned the USB cable connectors with lighter fluid (or can be done with any other solvent) to remove any grease.
5. Disabled 'Selective Suspend' by using a registry hack.
6. Used an SSD drive for System paging file.
7. Disabled ALL CPU power saving optimisations in BIOS. C1E state, C3, C6, C7, EIST Function, Intel TurboBoost®, Thermal Function, etc etc etc.
8. Double checked voltages fed to motherboard components with multimeter and increased the voltage where necessary (DDR3 Memory +0.04V).
9. **Downgraded the Virus TI back to OS 4.0.5.01 because anything after that causes the arpeggio to play out of time by -11ms no matter what I do. I will NOT upgrade to the latest version until it is fixed. See THIS THREAD // SAMPLE MP3 // SAMPLE PROJECT (with extras)
I hope this chunk of information helps others who have had similar problems.