Might they be fungus gnat larvae? Are you seeing any tiny flies swarming around the containers? You could try treating the soil with Bt. I hope at least some of your seedlings survive.

Hello Karyn1, No they are definately not fungus gnat larvae and there are no flying gnats at all. I think the heat of the propogator has hatched what was in the compost. I have repotted into fresh compost from a different supplier. I'm afraid the suppliers are getting very lax in their steralization and we are experiencing many weed and pest problems because of this.
Thank you for your comments.
Hazel.

I've had weeds pop up from large bags of potting mixes that I use for my outdoor plants but have never had any problems with the stuff I use inside or in the greenhouse for seeds and cuttings but they are in smaller bags.

I wonder if you could kill any organisms if you place the soil you are going to use for your seeds/seedlings in a sealed baggie and pop it in the freezer for a few days? The only thing that I've been dealing with are fungus gnats and they infest my trays after I've started the seeds or cuttings. They are miserable and difficult to control. Good luck.