Had you been running outdoors prior to the gym sessions? The gym can be very boring and demotivating in itself - I know because I'm stuck on the treadmill druing the summer (too hot to go outside here in Dubai). Now it's a bit cooler I run outside and I can't bear the thought of ever having to use a treamill again!
Wear headohones and listen to your fave music to get you going. Don't overdo it. Walk and run, walk and run if you have to or do some cross training for a few days, to work new muscles, and then go back to running.
If I ever feel like I don't want to go for a run/workout I tell myself how much better I will feel after __ minutes of exercise compared to __ minutes in bed/sitting on my backside/watching the box etc etc. In relative terms this makes me motivated.
Doing 10 minutes of something is better than doing 10 minutes of nothing.