Tournament pairings

[Random-Man]

I couldn't find an answer to this anywere, and sorry if this question is in the wrong section, and if so I will re-ask it in new Q&A.

What happened is that the software paired both undefeated people down for the last round.

there were 5 people in this tournament.
Player A against B - A wins
C against D - C wins
E with the bye

ok round 2 is paired this way

A against C - A wins
B against E - E wins
D with the bye

final round 3, this is were it gets weird
So far the points look this:
A-6
B-0
C-3
D-3
E-6

the first time it paired it said this:

A against D
E against C
B with the bye

we deleted round 3 and repaired and it looked like this (the way it should be):
A against E
C against D
B with the bye

I suspect other factors influences the outcome of the pairings.
What does the selection 'Double Loss' mean? Does that matter or effect anything? When I was at GenCon and the last Chunin, it didn't matter if you went 2-0 or 2-1 or 2-0-1... so whats the point of the double loss selection?

Could manual pairings in either round 1 or 2 effect the automatic pairings for round 3?

The two undefeated people should be paired against eachother right?
Why did this not happen the first time?
Did we take the correct corse of action?

Thank you for your time!