Yes they do.  I think that on the SF 86, it states that you and your employer must be contacted.  This policy applies to your past employers as well.  If you have been fired due to theft of other crime(s), you might have to explain why, in a personal interview, committed such an offense.   

You know, its a security clearace, you become an open book for whom ever is conducting the investigation.  And then, the polygraph is waiting for you.

Good Luck!

     The form only goes back seven to ten years.  However, the actual investigator can look further into your past if he/she feels it is necessary, or acquires some information that may warrant their checking into your past further than what the form requires.  I have also noticed that depending on the agency for which you apply, there are additional forms they may have you fill out that go extend the period to "In your life have you ever?".  Polygraph examiners of course will follow the latter line of questioning.