well, I will say that hackers software generally messes up the fta stuff and sometimes to the point that using the serial/usb interface to reload factory stuff does not always clear out the bugs.
jtagging is used to reprogram the chipsets without using the interal software loaders. Seems that most pansats have interfaces on the board (have to open it up) for just such a need. I know I bought a pansat 3500 (ebay, $80) that no matter what I did it still had issues, until I got a 20 pin cable, some software and the code files for the particular chipset that was in my 3500. After I jtagged it, I could then reload factory software normally and the unit worked flawlessly afterward.
If you are not afraid of electronics or working with some loader programs on your PC, jtagging is actually quite easy and an inexpensive way to grab a nice receiver on the cheap since the seller thinks it's useless.