Hi Joanna, glad to hear it is not the instrument. The Hammond 44 has an inherently low output, this has been discussed many times here, especially when using special effect pedals. As you mentioned, you were able to get more gain when you use the signal out of your amplifier to your recording unit, this is the same as D.I. pedal. Also when the boost pedal is connected from the melodica to the amplifier, you will notice a substantial volume increase. If you ever do decide to get a boost pedal, make sure it is a “Clean Boost Pedal” and not a drive pedal, very different.
Melodica-Me