title: Github thinks branches are different after merge
body: <p>I've banged my head against the wall with this Github issue enough to finally come here for help.  My <a href="https://github.com/KAPSARC/KTAB" rel="noreferrer">repo</a> has two branches of interest: <code>master</code>, which is the currently live release branch, and <code>alternate-testing</code>, which is exactly what it sounds like.  Our dev process has feature branches regularly branched (and forked) off <code>alternate-testing</code>, then merged back into <code>alternate-testing</code>.  Finally, <code>alternate-testing</code> is periodically merged into <code>master</code>.  Note that the testing branch is the gatekeeper to <code>master</code> - nothing gets into <code>master</code> but by going through <code>alternate-testing</code>.</p>
  
  <p>To be perfectly clear, this is not a situation like this:</p>
  
  <pre><code>1 -- 2 -- 3 -- 4 -- 5 -- 6 -- 7 -- 8 [master]
         \                      /
          A -- B -- C -- D -- E [alternate-testing]
  </code></pre>
  
  <p>as in <a href="https://stackoverflow.com/questions/27413038/github-branches-are-always-ahead-or-behind">this question</a>, because master <em>never changes</em> by itself.  A more relevant diagram is:</p>
  
  <pre><code>1 -- 2 ---------------------- * -- 8 [master]
         \                      /
          A -- B -- C -- D -- E [alternate-testing]
  </code></pre>
  
  <p>So at the end of this diagram, <code>master</code> and <code>alternate-testing</code> have to be identical.  There were no changes to <code>master</code> after the branching, and every change in <code>alternate-testing</code> has been merged into <code>master</code>.</p>
  
  <p>Yet, GH shows that the two branches are out of sync.  I just did the merge this morning, and GH says about <code>master</code>: "This branch is 3 commits ahead, 29 commits behind alternate-testing."</p>
  
  <p>How is this possible, and how can I fix this maddening problem?</p>