Actually what you are seeing isn't a glitch - it is designed to work this way. May seem a little strange, but here's the skinny:
The Adjust Rankings dialog is meant for you to be able to easily "fix" the bust-out order when you accidentally bust players out in the wrong order. This happens a lot, and previously the only way to fix it was to undo the wrong bust-outs (and there could be many) until you get to the first wrong one, then bust the players out in the correct order. This could be painful.
The Adjust Rankings dialog was added to make it easier. Just click a button to move a player up or down in the rankings. Since rankings are based entirely off of bust-out times, when you move players around in the rankings, the software has to change their bust-out times. Now, it could have been done such that you, the user, would have to change the times manually for players you wanted to adjust, but that's nearly as painful as the old solution (of undo-ing and re-doing bust-outs). Instead, the software adjusts the bust-outs times for you when you move a player in the rankings.
But when you move a player, what to adjust the time to? The software has no idea (and probably the user doesn't either), so the software chooses a time halfway between the 2 players. For example, let's say we have 4 players who busted out like this:
Oops, we should have busted Charlie out instead of Bob. So we move Bob up one in the rankings. This becomes:
One could argue that perhaps the software should have just swapped the bust-out times of Bob and Charlie, but it gets a bit more complicated when you add the fact that there can be chops.
In your case, you were moving a player to the bottom of the list, so between what 2 times was it placing the moved player? Between the time of the chop (the first bust-out) and the start time of the tournament.
If the times are not accurate enough for you, you can always manually adjust the player's bust-out time. There is an option to do that on the Adjust Rankings dialog.
Now after having explained all of that, it seems to me that this shouldn't be an issue for you at all, unless I am understanding you incorrectly. If your league awards points for simultaneous knock-outs, why do you bust the players out together and then go to the Adjust Rankings dialog and separate their bust-outs? This basically does the same thing as NOT busting them out together. That is, it is the same as busting them out one at a time.
If you want to signify that they busted out together, yet rank them according to chip stack, you should bust them out together and then go to the Prizes tab and edit their Chop. (The Chop dialog will display automatically when you bust players out together ONLY if there are prizes associated with the ranks they will achieve. Otherwise, a chop is created but not displayed.) Go to the Prizes tab and press the Chops button. There you'll see a chop for those players (it should be a light-gray color indicating no prizes). Edit the chop and set their appropriate ranks there. This will still have the players busted out at the same time, yet rank them separately.