I received a Garmin handheld GPS for Christmas and have taken it on several rides. When compared to my buddies altimeters we always have different measurements even though we all calibrate at the start of the ride. Our end results on total altitude climbed can be off as much as 25%.
Another issue I have noted is that when a large truck or vehicle passes you and you get that air blast, it causes a big spike in altitude which immediately calms down after the turbulance dissipates. But the total altitude gained totalizes it as if it were climbed. I even drafted in a pace line on a flat road and saw an 18 foot rise in elevation due to the negative pressure created by the guys in front of me. I would get out of line and immediately lose the 18 feet. My buddies saw similar results.
Are there any truly accurate altitude devices out there? GPS would be inaccurate because of GPS drift. I could always take the transit but that would put me over the weight limit for my bike.