Don’t know if this is the same as your issue, but it sounds like it could be. From the Mesa Boogie board:
"Dear MESA/Boogie JP-2C Owners,
Feedback from all sources in the musical world is important to us, but none more so than from our own customers. We’ve been watching the feedback regarding the JP-2C from several of the popular forums, and while we are deeply flattered by most of it, it’s come to our attention there is a potential for mismatched Effects Loop levels between the Channels for some players under certain settings conditions, particularly those that use the amp at lower volumes. Consequently we have a voluntary update that addresses this possible discrepancy and creates more balanced Loop levels throughout the Channels when the amp is used for its intended purpose (a Clean sound in Channel 1 and two high gain overdrive sounds in Channels 2 and 3) at these lower playing volumes.
The feedback suggests that for many, the Effects Loop is operating satisfactorily and within the performance parameters needed. Those players may not want to part with their amplifiers for a week or two to receive an update even with the shipping cost covered and the update free of charge. For those of you experiencing difficulties matching levels, we can send a UPS Call Tag, have the amplifier picked up and update it and return it to you within a week (shop time) free of charge. Regardless of which of these categories you might fall into, should you be unable to be without your amp or simply choose to wait until time permits that, rest assured we will be happy to do the same for you or subsequent owners at no charge any time during the 5-Year Transferrable Warranty.
The update addresses the concerns most commonly associated with the feedback we have noted on the forums. These concerns arose in applications where the playing volumes were low and/or a high setting of the MASTER in Channel 1 (as compared to Channels 2 and 3) produced excessive volume in the first repeats using a Delay. The update addresses these concerns and provides a well-matched Effects blend–again–when the amplifier is used for the intended use stated above and the Channels are relatively close volume-wise.
However, since performance of the Effects Loop is greatly affected by the settings of both the preamp (GAIN and Tone Controls) and power amp (MASTER and PRESENCE) in each of the Channels, it is still possible to experience SEND and/or RETURN level differences under certain conditions. Namely those which deviate from the Clean/Gain/Gain Channel dedication noted above and/or extreme GAIN and MASTER differences Channel to Channel. In an amplifier with this much GAIN and output power, as with any hot-rod, an application must be determined and a relative tuning for that application applied to achieve stability for the widest number of “drivers”.
We are very sorry for any inconvenience this may cause and appreciate greatly your willingness to help us address this concern early on and assure the greatest level of satisfaction from your new amplifier.