So, you must have bridged a solder joint or something without soldering anywhere to it? Well that's the problem then.
JDM-055 schematic is here on the forums, have a look. The 4 ADC lines for the sticks, LSX, LSY, RSX and RSY really have nothing to do with each other, aside from using the same 3.2v and ground, and if those had an issue every axis would have an issue.