Well, that's kinda what happens if your input is set to L+R sum....as I mentioned earlier. Voltage from your pickups is cut in half, -6dB. Set it to L only. You never responded to whether you checked that input parameter or not. Input trim on the II and the older units is very different, you can't use it as gain on the II...as I understand you could on the older units.
+1
trazan is correct here, in that there have been a number of suggestions given, yet the OP has not continued to fill us in with much detail as to what he's tried different (if anything), whether he has switched guitars, guitar cables, MIDI pedal being used, tried a different monitoring source (headphones or other), nor disclosed what he is listening on currently for FRFR amp/speakers (are these cheap $100 home studio monitors or something more pro-level?).
joetdc, do you have alternate equipment available with which to test your AxeFx? If so, here is another suggestion: record a guitar track using some kind of preamp, direct, totally dry (not using the AxeFx), by any method you have at your disposal. Then, assuming this is a pure analog process, run this recorded dry track into the REAR input L of your AxeFx (make sure that your input I/O is set up properly to accept Rear L input). It may not be a perfect way to test things, but it should help you determine if the AxeFx is working properly (at least from the rear input), and it also should allow you to adjust the INPUT gain (assuming you have an analog mixing board sending the recorded source to the AxeFx) to your satisfaction in order to eliminate your concerns that there isn't enough source going into the AxeFx. You can also compare this "dry original" track running through the AxeFx with GLOBAL BYPASS engaged to see if it is TONALLY being altered, and as a means to compare/adjust input gain.
Where are you located? Remote area? or are you near any major city? If so, there may be AxeFx users in your neighborhood who have the time to give you a little personal assistance - or - you may even want to try bringing the AxeFx to a local music store in order to audition the axefx on different powered monitors, and with a selection of different guitars. I'm sure that if you do this during a "down" time at a music store, they'll be happy to indulge you and check out your cool new toy, that they've probably heard of but never gotten their hands on. Just throwing ideas out for you to consider.
I feel ya, but sometimes this stuff happens. You gotta roll with it until you have enough info to make a sound conclusion.