When running MSTest from Visual Studio - the unit test execution time is relatively quick.
When running MSTest from the command line, with /testsettings flag - the exec
Have you tried disabling deployment in the test settings? When it is disabled, the tests should be run in-place rather than on copied assemblies. (See http://msdn.microsoft.com/en-us/library/ms182475.aspx for details.)
try MSTest.exe /noisolation http://msdn.microsoft.com/en-US/library/ms182489.aspx