Hi Nick,
Sorry to hear of the issues, but I am happy to help find a solution.
Lets first Optimize your PC following this guide:
https://support.focusrite.com/hc/en-gb/articles/207355205-Optimising-your-PC-for-Audio-on-Windows-10
Since you have the 2i2 (2nd Gen) can you tell me which driver you installed for the unit?
If you have not installed the driver more conducive to using Pro Tools First (which is the 4.12 driver) please remove the currently installed driver from Programs and Features and then install this driver with the unit disconnected:
https://support.focusrite.com/hc/en-gb/article_attachments/206158489/FocusriteUSBInstallerPT1st4-12-1-131.exe
Once installed please test again. If you should find that the behavior returns it will be ideal to also look into DPC Latency.
Since WIndows is not a "real-time" operating system it issues Procedure Calls in which drivers are given a chance to execute and do their jobs. If drivers are out of date or if components are not functioning well within the system, the execution times of the drivers can be too long and prevent other drivers from having the ability to do their job.
Can you download this program, LatencyMon, and run it while playing audio at the same time, making sure to actually replicate the problem.
https://www.dropbox.com/s/5ff671c5n2adr0y/LatencyMon.exe?dl=0 (LatencyMon)
Please also go to the Drivers Tab, sort by Highest Execution, with the highest on top, and post a Screenshot of that page.
http://www.wikihow.com/Take-a-Screenshot-in-Microsoft-Windows
Once I have a bit more information, I can aid you further!
Best regards,
David // Focusrite Technical Support