I'd have to agree with Baradium on this one. GPS units are receivers. Unless there is a problem with a unit having RF interference with the nature of the electronics, there should be no problem with multiple in the aircraft. It is possible you had a faulty unit, or the antenna for one was in a poor location. The more satellites visible to a unit, the greater the accuracy. If the handheld unit was having a problem seeing satellites due to the metal structure of the plane and no external antenna, that would explain it's innaccuracy compared to the panel mounted one.
Mine came with a warning about errors if too close to another GPS receiver. All antennas and receivers actually emit the signal they're receiving. An antenna is a passive signal amplifying device, and part of the amplified signal is emitted. Likewise the first stage of any RF receiver is an electronic signal amplifier. Some of the amplified signal is again emitted. What can happen with two GPS receivers, or even FM radio for that matter, if close enough they will receive not only the source signal (from the satelites) but also a second signal from the other receiver. The second signal is just slightly out of phase with the source so you get distorted information. This caused us all no end of frustrations when building amp circuits in the basic electronics labs, until the prof explained we were causing interference with each other. 
When using dual GPS systems, they must have shielding from each other and use a common antenna, or have the antenna's carefully located to prevent interfering with each other. Hand held units aren't designed for that.
Phil - Electrical Engineer
I don't doubt your credentials or knowledge on the issue at all. I just suspect that since it seemed to be a consistent error that it was likely from a more stable interference factor such as the airframe shielding satellite visibility that from any local sources. Granted, on the antenna issue they do have the tendency to have some feedback potential, though I've only seen that in situations where higher power was involved, and proximity was extremely close.... unless there was a defect in the shielding or in the electronic circuit design or component failure that generated an RF wave harmonic allowing for distortion potential.
In any case, this would be a situation of debate in a vacuum since we have no direct ability to examine the plane, nor the unit. Can you hook up the handheld unit to the external antenna and get the distortion to disappear? How about with it outside of the aircraft? If the distortion remains, there may be an internal error.
As already noted, VFR units don't have the accuracy of IFR rated ones, and panel mount will, obviously, give the best results versus handheld units of either VFR or IFR types due to the magnetic anomaly and signal leak survey mapping required for a proper panel install.
If you go to AOPA's website, the Air Safety Foundation sub-site there has a series of presentations on GPS for VFR and GPS for IFR, describing the systems, accuracies, and other factoids that may be of assistance to clearing up this anomaly to an extent as well.
Please understand, we are simply offering advice for the sake of assistance. Not challenging you.
