I'm doing a low carb, high fat diet (LCHF) and im back into the running too. I know that the first week of the diet a lot of people lose 'water weight' and then you've got to let your body settle to the big change you've made! I think the problem is low carb is basically advertised as a quick way to shed weight but in reality it's different for everyone (it's just the amazing success stories you always hear about rather than the ones that took longer!)
I'd agree that you might have gained some muscle too!!
One thing I can vouch for so far is my energy levels are way more consistent and I've had no trouble running eating this way, if anything I'm running better now distance wise, if just a tiny bit slower! I'm not promoting this way of eating because it won't work for everyone and my diets quite strict at the minute, it seems to be working for me personally though.
Just keep going and you'll see the changes! Good luck!
P.s I refuse to weigh myself in fear il be on the scales 3/4 times a day plus they're not going to tell me how much fat I've lost and how much muscle I've gained instead!!! I'm just going on whether I can get back into my fave jeans