At the begining of OWB Klein hints at a bonus for completing your quest quickly, what is this about? Is it the transportalponder, or something else and is there really any difference if you take your time?

The transportalponder is the only way back to BIG MT, so that's not it. I really doubt there is anything. Why would the developers punish you for taking time and exploring.

I wondered this myself. However I took my sweet time since I was under the wrong impression that you had to get everything done before the end of the game so I figured I missed the reward.

Considering that when you do the tests with the stealth suit you recieve a reward which is deposited in a safe in that lab I am assuming that perhaps there might be a good reason for the safe in the Sinks/ Dr Mobius's bedroom.

Or I could be totally dead wrong.

I've ran the dlc 3 times one only took 45 minutes and nothing special was given

It must be the transporterponder and Klein is just trying to rush you along. That's the best I can figure for now unless there's a bug, but that would be unheard of....

I think that was put there to give a sense of urgency to the otherwise hilarious and lax environment that is OWB.

Ummm isnt it obvious? HE WAS LYING, just like he did about putting your brain back in duh xD
and now a qoute from your in-game brain: "you didn't actually believe them did you?"