I also have a Surface Pro and I experience the same issue, but I use DisplayLink at home and a displayport connection at work. The problem occurs with both monitors and is most definitely a problem with the new scaling options in Windows 8.1.
The problem is an old problem with scaling on Windows, requiring that you log out and log in to change you scaling options. In the past you could only have one scaling option for all monitors or you would have to manually change it every time you switched.
With 8.1, they are trying to address the issue of high resolution monitors and small screens. Unfortunately, they have not figure out how to accomplish this completely without us having to log out and back in. What we get instead is a hybrid of whatever scaling we selected for a monitor which typically looks awful. Some screen elements too small, some very fuzzy and some too big.
I have found that I can set a different scaling for each monitor and Windows 8.1 will remember. I have also found that it works best if I have the internal display disabled when attached to another monitor. Finally, I log out before undocking and log back in when accessing the Surface directly.
Too me this works better since I find the Surface a lot easier to work on when the scaling is set to large.
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