I've found tube extenders for my Hed's to be a total pain in the *ss. You lose them, they leak, etc. Try these - you'll never go back to tube extenders. They solved all my problems(which sound similar to yours). Ideal for tubulars w/ deep rims. the valve tool also works great.
http://tufonorthamerica.com/accessories.php

I gotta disagree with jaylew. I like the simple "tube" extensions. The nice thing about these extensions is that they don't interfere with the factory valve core/body junction. There is also just a single seal that could leak, that being the factory valve core/body junction. There is also the junction where valve meets extender, which is where virtually all of the leakage takes place. When you use the extenders that go between the factory valve body and core, you now have two seals on the extension. Hey, whatever works for you, but i've got to wonder if you've ever actually tried the other kind. I used the "tube" extensions for a few years and before almost every race I did, I either wound up at home cursing while applying yet another layer of teflon tape, or searching for someone who would hold the pump head on the valve while I pumped as hard and fast as I could trying to outrace the stream of air coming out. During one such panic the morning of a race I was about to give up and use my training wheels instead when I realized I had one other option - to try the extensions I had ordered with my tires. Worked beautifully and I will never go back. I have never experienced any leakage. What I like is that you can place the pump head on the valve, where it's supposed to be. This simple change has been as important to me as a saddle or pedal switch.

Yes, they can "leak", but that's just when inflating the tire. In my experience, they will leak. Not all of the air from the pump ends up in the tube. (Although I still have no problem inflating this setup with a single CO2 cartridge) But they have no impact on whether or not the tube will leak air through the valve. Since these extensions hide the valve, you have to leave the valve unscrewed and you can't deflate the tire without removing the extension. This bothers some. I'm not trying to start a valve extension war here, I just have very passionate feelings on this topic.