I upgraded from Resharper 3.0 to 3.1 today and immediately had some issues.
Issue #1 - Intellisense was disabled.
My intellisense was disabled on the Visual Studio level. To re-enable it, I went to Tools -> Options -> Text Editor -> C#. In the Statement Completion control grouping, I checked "Auto list members" to turn it back on.
Issue #2 - Alt+Enter stopped working.
To fix this, just go to Resharper -> Options -> General. Then select the "Visual Studio" radio button under "Restore Resharper keyboard shortcuts". Then click "Apply"
Here's another handy tip. Since Resharper won't play nice with the new .NET 3.0+ features until version 4.0, you can temporarily disable/enable it on any open file with the Ctrl+8 keyboard shortcut.