Tonester,
The problem is one fork is underfilled, and has air in.. This creates a postive spring preload and causes the rode to exstend all the way..
This reelates back to a ealier string but if you want the rod to exstend all the way out with no addtioanl load, don't completly purge the clyinder.. Purge the cylinder with the spring a few turns out... Then purge and seat the spring... Now the fork will exstend all the way... If you doing SX its cool but for mx this is a bad idea.. Check out my rebuild instructions for you fork..
Regards,
Jer