If you're using a Windows Mobile version of Run.GPS, you can configure an altitude offset value in Main Menu > Configuration > GPS Config > Altitude Correction > manual value
During a 4500 km bicycle tour this year I discovered that Run.gps on my HTC Touch Cruise consistantly showed my current altitude as 40m above the real figure. At the top of most mountain passes and while at lakes etc I would check it. I presume a hardware fault? Not sure if this is unique to my hardware or not, but it would be good to be able to calibrate altitude to compensate.