I have the exact same issue.
I thought it was a problem with the dock, but same thing with a new one.
I've noticed that USB and network disconnects/reconnects when the surfacebook is heating.
Example :
Programs lounched :
- Outlook
- Google Chrome
- Sublime text
I launch Photoshop, the fans begins to speed up (I hear them clearly), and here begins the disconnect/reconnect.
After the photoshop startup, fans slow down, and the disconnect/reconnect stops...
I think it's a overheating problem with the surfacebook, who disconnects the dock connector, without any solution...
Following that, it's normal that disconnecting the dock and working directly on the surface resolves all problems...