Poweragent merge cuts data

I recently got a powertap off ebay and it works great.  The only issue is that when I finish a ride with multiple files, sometimes when I merge the files together the combined file shows fewer miles covered.

For example, on my ride this morning, the tally for individual files is 20.78 miles(which is close enough to correct).  However, if I merge, the total distance shown is more like 16 miles.  So somewhere is just decided to lop off 4 miles.  Also, it results in a moving time that is greater than the total time.

The four files were a result of various stops, and below are where I created a separate interval:
1) Started out from the house and created an interval right away.
2) Intentional stop 12.8 miles in, created interval when I stopped, and another interval when I started again a few minutes later.
3) Intention stop after another  2.6 miles.  Manual intervals not created, the but LYC created a separate file due to length of time stopped, and there is an interval0 and interval1 that show in poweragent.
4) Long stop @ traffic light after 3.8 miles.  Manual intervals not manually created, but LYC created a separate file, and there is an interval0 and interval1 that show in poweragent.
5) Final leg of 1.58 miles.  Manually created interval upon reaching home.

At this point, although I'm a little confused by how it counts intervals, I'm more concerned with the merge function just willy-nilly knocking off mileage.  With the merge, it is difficult to analyse power data to get accurate values like nominal power.

Anyone else run into this?