[BScout]

Originally Posted by ArthurSchwieger

It seems that Pro Tools is somehow generating this and sending it to the computer and not through the audio interface.

This is not possible.
Pro Tools can only talk to one interface (it does not support multi-interfaces; the whole engine does not have this ability.) ASIO4ALL can combine interfaces but that's about it on Windows. And hopefully you are using the Scarlett's drivers.

You have computer problems not Pro Tools problems.The Scarlett is multi-client which means it can accept multiple sources to it. In this case, your computer as an additional source. Which is making its own sounds which you've attributed to Pro Tools -- something Pro Tools isn't doing.