Mike is on the money here. There are a lot of reasons this can happen, but the most common is that the flatness of the bottom of the saddle does not match the flatness of the bottom of the slot in the bridge. Martin cuts the tolerances in the bottom of the slots nearly perfectly every time, so it is most like that the bottom of the saddle needs to be flattened properly. A simple way to do this is to tape a sheet of sand paper (180 grit or higher) to a very flat surface (grit side up). Take a sharpie and cover the bottom of the saddle with a black mark. Now, keeping the saddle dead perpendicular to the sandpaper (sharpie side down), start sanding the bottom of the saddle till the sharpie mark is completely gone. It should not take long (a few minutes) and you should end up with a very flat saddle bottom. Keep in mind that this CAN remove a good bit of saddle if you are not careful and lower your action more than you might like.
It is also possible that the pickup was installed improperly and it is (as Mike stated) shifted toward the bass side. However, if this is the case, the pickup may have been installed improperly and might need a look from a good guitar tech.
It is also very possible that the piezo crystal is slightly damaged (it does not take much and could have been that way since it was installed).
Then there is the possibility that you have an aggressive setting on the amplifier (parametric EQ?) that is omitting the frequencies associated with the high E string.
One last thing that can cause this is that the action on the guitar is extremely low and there is very little saddle left. This can cause a very low break angle between the String pin hole in the bridge and the top of the saddle. This, in turn, can cause very little pressure between the string and the top of the saddle resulting in a very low output. The remedy for this is usually slotting the string pin holes along the top of the bridge just behind the saddle (between the saddle and the string pin hole).
Try flattening the bottom of the saddle properly first, that is your most likely culprit.