Michael, sounds like you've got sciarid fly. its their larvae that damage the roots, the adult flies don't cause any damage at all except for being unsightly. during warmer months there is a bio-control mite readily available from organic gardening cataologues. but these don't work in colder weather. most sites will tell you that there isn't a chemical registered to kill them, but you can make a completely organic one using (can be bought, but is expensive) Feverfew (Tanacetum parthenium) flowerheads - the chemical in them is PYRETHRIN - it basically kills any creepy-crawly it comes into contact with so be careful if other beneficial beasties are present. dry the flowerheads, grind them up, mix with water & washing-up liquid (use an ecologically-sound one), spray. treatment may need repeating on a weekly basis as the larvae turn into adults, but should help get things under control. I understand that your plants like being damp, but try not to over-water & consider watering from underneath as this may have an effect; as far as i know its not anything to do with the compost source/type
hope this helps - wendy