Need to know wattage of LED bulbs.
What I have done in the past is use one halogen in the circuit with GU10 LED bulbs. Using this setup it seems to work fine though you won't get below about a 15% dim on the leds.
Remember the X10 lighting modules all have a minimum load of 40W.
Transformer problems could be due to minimum loading as well. Often these days MR16 halogens come with their own transformer. So we have found connecting several LED bulbs to one transformer normally does the trick.
Did you buy dimmable versions of the bulbs. Or non dimmable. We have often seen huge amounts of flickering when people try and use non-dimmable on a dimmable circuit.