Thumpy Sounds

I've been doing some recording with my acoustic-electric J185 plugged straight into the board. The tone sounds really nice, but there's sort of a muffled sound in the background, not a tone so much as a rhythmic thump in the air. After I heard it I made sure I wasn't beating on the top or damping with my palm, but it's still there. Any ideas on what it might be? Should I unplug and put a mic on the soundhole?

Why not try with a mic and the guitar plugged in, record both and see if you can pin it down ?, sometimes juggling between the two might even yield a nice sound you can use.
If you are miking it don't put it directly in front of the soundhole, rough rule of thumb is that it will sound progressively less bottomy (thump?) the closer you get to the headstock, sometime pulling away from the guitar helps to 'expand' the sound too.
When you find it --- write it down in case it happens again.

That is generally life recording with piezeo's.
You have a contact mic on a the vibrating soundboard- it is going to vibrate across a wider frequency range than you perhaps wish it to.
The solution:
Try a High Pass Filter, 12db/oct or higher around 80-120hz.

Or use a mic alone.

Here is a little discussion we had last month:

http://www.tdpri.com/forum/recording-progress/100369-recording-acoustic-guitar.html

Hope this helps, it helped me.

Dan

Thanks guys! I'll let you know how it goes.

Is the sound rythmnic? If so does it pulse or does it seem to remain in tempo with your playing?

If it's the latter it could be a noise that you are creating so check that you are not rocking the guitar against your body or fretting hand and that your strap is not moving against the guitar.

Also check the lead as they can pick up various sounds including movement.