There is a bug in the upgrade process when converting a LINQ to SQL designer (.dbml) file from VS 2008 to VS 2010. They changed the implementation to hold the layout information in a .dbml.diagram file rather than the .dbml.layout file. Instead of just renaming the existing file, it replaces it with a new one effectively loosing all of the layout customizations you may have made to the design surface.
Luckily there is an easy fix. Just delete newly created .diagram file and then rename the old .dbml.layout file with a .dbml.diagram extension. If you want to be safe, you can rename the first .diagram file rather than deleting it. When you open your design surface now, your original class layout should be back.
I'm told by the product team that this will be fixed in the next release. That's why it's called a Beta release.