Hi Dave.
Excellent points. Yes, the out of phase phenomenon is something that could certainly explain the problem as sam has been describing it (I've personally experimented with phase/out of phase stuff and can attest to the center channel elimination of sound). In fact, if you use the synth to play a sine wave on one Tone and an inverse sine wave on another Tone, you'll hear nothing when you play a key (just as a demonstration).
Anyway, with regard to your response to my balanced/unbalanced suggestion, there is actually a significant technical difference between a balanced and unbalanced signal (in terms of electrical design and thus in how the two are handled by sound equipment). An excellent explanation of the differences can be found here.
http://home.btconnect.com/woodgreen/tech_tips/techtip/art6.htm
but as a summery, unbalanced (2 wires) relies on a zero voltage fixed reference point, thus you have ground and "hot" wires. A balanced signal has 3 wires, ground, "live" and "return." The "live" wire sends the in-phase audio signal, the "return" wire sends the 180 degree out-of-phase audio signal and the difference between the two is taken as the reference voltage while ground is used for grounding between the two devices. Now, if you have a Tip-Ring-Sleeve jack in your Fantom-X (which you do) with an in-phase signal sent on Tip and 180 degree out-of-phase signal sent on Ring (and Sleeve acting as ground), then you use a Tip-Sleeve cable to plug into that jack, what happens to the Ring connector? It touches the Sleeve on the cable plug, the ground contact in the jack is also touching the Sleeve on that plug. (Note your earlier discussion about phase differences and how they cancel each other out). If the output device (the Fantom-X) is using an electronic balancing method (via integrated circuits), which I believe it is (as opposed to transformer isolated balancing), the "return" signal becomes grounded (somewhat muting it) and the output level will be cut by 6 dB when using a TS cable or an input with only a TS jack. This is a 2 times level cut! I've experienced this problem myself before and had to switch to balanced cables because of it.
Regards,
Nathan Sheldon
http://www.nathansheldon.com/