In  Microsoft Test Manager (MTM), some of the issues which people face while trying to pause a test and resume testing are:

Issue 1:

When someone pauses a test and clicks “Save” or “Save and Close” the test is marked as “Passed” instead of being “In Progress”.

Resolution:

This is the default behavior if the test contains no expected results.

Also, Microsoft Test Manager (MTM) has a discoverability issue. If you want to leave the test “In Progress” don’t click on “Save” or “Save and Close”. Instead, click on “Return to the Testing Center” button which is next to the “Save” button in the Test Runner.

Issue 2:

When someone pauses a test and clicks “Save” or “Save and Close” the test is marked as “Failed” instead of being “In Progress”.

Resolution:

This is the default behavior if the test contains some expected results.

Microsoft Test Manager (MTM) has a discoverability issue. If you want to leave the test “In Progress” don’t click on “Save” or “Save and Close”. Instead, click on “Return to the Testing Center” button which is next to the “Save” button in the Test Runner.

Issue 3:

When someone pauses a test and returns to the Testing Center, there seems to be no way to return to the Test Runner.

Resolution:

Microsoft Test Manager (MTM) has a discoverability issue which is mentioned here http://blogs.msdn.com/b/gautamg/archive/2011/06/02/faq-how-do-i-resume-my-manual-test.aspx

Issue 4:

When someone pauses a test, returns to the Testing Center and closes MTM, there is no way to return to the Test Runner.

Resolution:

There is no resolution for this. You will have to make sure that you don’t close MTM if you want to resume testing.

Issue 5: 

When someone pauses a test, returns to the Testing Center and tries to run another test, he/she is asked to save the results and the first test couldn't be left in the paused/In Progress state.

Resolution:

There is no resolution for this. If you are blocked on a test and want to run another test, then don't pause the first test. Instead, mark it as Blocked. This way you can execute the second test and when you are unblocked on the first test, you can mark it as Active and run it again.