The merge will have different DPS numbers some times, which is intended. Here's an example.
On your own log, you're fighting, doing awesome DPS, then die half way thru the fight. We don't get a boss-kill event in your log (it only shows up in 1 person's log, likely the one who got the killing blow). so on your personal log, you'd have a nice DPS number, let's say 1,100.
Then we merge logs, and we see the fight lasted 50 more seconds after your death. We recalculate your DPS number with the new 'timeline' and it will end up lower, say 930 DPS, since you can't DPS while dead.