I have now checked the first 10 episodes. Ep 5 (Vows) is short because it aired at the same length. Ep 7 (Doppleganger Part 2) is short because the recap isn't on the DVD. Unfortunately Ep 10 (Sleepers) was short on TV (42m 52s without the in-credit trailer for next episode), but yet another...
I have the TV recordings. First impressions suggest the DVD's have edited episodes, as some run for 41 or 42 mins, whereas most seem to have the expected 44+ mins. I will be doing some further checking.