When is a short not really a short?
Swap your positive and negative meter leads.  Do you still read a "short"?

Check the power consumption of your board when powered, or better yet, put it on an adjustable current supply with the current limit all the way down and see how far you have to turn it up to get out of current regulation mode and into voltage regulation mode.

Most likely your jtag problem is unrelated to the meter reading.  If you can't pull some of the parts out of sockets, try slowing the jtag clock.