When you say three way, do you mean three gang or is it part of a two way switching circuit?
One of the main problems with dimmers or lamp timers is that with no neutral being used, they rely on a small leakage current through the lamps to operate correctly, hence the specified minimum load. Not all loads are the same. The easiest is a filament lamp, purely resistive - the most difficult is a complex load like an LED or an electronic transformer.
I had a similar problem when I replaced three CFLs with three GU10 LEDs - the LEDs would not operate correctly. The only answer and a poor one, was to put one of the CFLs back. Some dimmers are not compatible with all LEDs. I had huge problems with a Lightwave RF dimmer and LED loads. I used the LEDs recommended (Aurora) but it still flickers, does not dim very much and I would never buy another one. It seems pointless to buy low energy lamps then have to add another load to get the dimmer to work.
With the two way switching, I eventually got a neutral to it and came up with a complex circuit that switches all loads and the three LEDs are back. Some manufacturers like Timeguard now offer an add-on device to overcome the problem.
If you still get the problem with say 60-W filament lamps, then the problem is with the dimmer or wiring. Maybe put the three way switch back and start again