Tagging Up on a Bobble - with a Twist

Question
I read the post entitled "tagging up on a bobble" (http://en.allexperts.com/q/Softball-2562/Tagging-bobble.htm) and it makes sense.  However, I had a situation tonight where I'm not sure if it applies or not.

There was 1 out, bases loaded, guy hits a fly to shallow right.  The ball hits the 2nd baseman's glove, but he bobbles it and it drops, but our right fielder dives and catches it before it hits the ground.  One guy bobbles, another guy makes the catch.

So, of course we get the one out (the catch), but all runners left as soon as it hit the 2nd baseman's glove (and prior to the actual "catch").  We threw the ball to 2nd base since we didn't think their runner tagged up, and the Ump called him out.  Double play, right?  NOT!  Ump thinks about it for literally 5 minutes (in the meantime we are already in the dugout getting ready to bat), and with some help convincing him from the other team that he was wrong, he CHANGES THE CALL!  Tells us to go back on the field, awards them 1 run (the guy that was on 3rd) and puts guys on 2nd and 3rd (for some reason...?).  

Really confusing.  We eventually lost the game by 1 run.  Any idea if the bobble/tag up situation was called correctly?

Your help is appreciated by the MB Dirt Shrews!

Answer
Hi Sebastian,

a runner on base can legally leave the base as soon as a defensive player touches ball that is going to be caught.

I use the example of a high line drive that deflects off a leaping F6's glove, carries into left field where it is caught by F7.  Runners can leave as soon as F6 touched the ball.

The umpire was initially incorrect, then corrects his mistake which we are allowed to do.  You've heard the expression "we want to get the call right".   The umpire then put the runners were in their opinion they would have been had the initial call been correct.  Which we should do.

Sounds to me like a overall good job by the umpire once they recognized they were incorrect.

Mark