To be honest with you, I have not had good experiences with the J-R programmer, It will often work at first use then all of a sudden give errors and not be able to be used as expected at times, I believe this is an issue with the bootloader mode, once in that mode its hard to get it back to normal "nand reading" mode, to be honest never figured out a good, prompt solution to get it back up and running normal, only because I have a nand-x and just reverted to it when I got into this situation. I actually returned mine to xconsoles for a replacement, of course been the good re-seller they are, they sent a replacement as soon as they received the one I sent them. Even with the new one I have the issue. The best thing is to leave it for a few days, once you have done that, try using it again, it should return to normal mode.
Honestly, while this may be a unlikely solution, as it seems I know, it requires no resoldering and potential damage and may work for you, just a heads up from experience.
I know all TX products are great, and they are, but as far as reading nands, the nand-x is the top shelf product, if you need rater and other advantages of j-r programmer, just be aware of these common issues.