Ok, you've got me confused now. When full extended you've got 100mm of stanchion showing? Try emtying the negative air chamber (schrader valve on the bottom of the left hand leg), this should return them to full height. Sounds like too much air in the negative spring, this will reduce available travel. If this works fill both poitive and negative chambers with the same air pressure. this should give you roughly full travel. I personally run my REBAs with slightly more in the negative chamber to make the forks more small bump sensitive but that's rider choice.
if on the other hand with no air in the positive spring (shrader valve on the top of the left leg) you still have 40mm of stanchion showing it's pointing to hydraulic lock or busted internals.
if all that fails I'd recommend a full service and change all the O rings, if you're not happy doing that yourslef send them to TFTuned. It' cost but at least you know they will be working properly when you get them back and their customer service is excellent.