First, make sure the sample rate in all software matches the hardware. From the list of things you've tried, I expect you are past this, but its a 'gotta'.
Next, call up Windows Resource Monitor. Its on the Start Menu, under All Programs Accessories>System Tools. See what's hitting your machine the hardest, be it CPU, Disk, RAM, or Network, using the graphs.
Be aware that Resource Monitor itself will create a load on the box. Once you have the issues down to one subsystem, you're going to have to roll up your sleeves and start looking into individual processes online to determine whats causing your audio buffers to fall short.
You might also try Focusrite Support. Hit them early in the morning, their time, and give them time to figure things out. Stay on em, but don't push too hard.
Hope this helps.