I saw the same thing in Prodigal. The city was basically under siege and Rodney didn't even mention Jennifer. Not once. No "I'm glad she's on Earth now" or "I hope that she's okay in the infirmary". Simply nothing. I would have expected... something after all the pining he did. On the other hand, he went completely "OMG, Sheppard, you'll get yourself killed, you idiot!" It's just the McKeller ship is either right in our faces, overwhelming everything else - or not there at all, so it makes no sense...

Also, as Jewel Staite said, she and David were more like brother and sister and it was painful and awkward for them to play lovers - and I think that it shows. Though that's just my personal opinion.