Clearlyif jtag is not writing successfully then something low-level is wrong. I can believe that fake flashing cwm touch onto a 3.0 kernel and restoring or wiping did something out of bounds rendering portions of the emmc inaccessible, but i would find it hard to believe this is coincindental emmc failure due to quality issues with the emmc. It is simply too specific, both in reproducability, symptoms, and prerequisites.
I have the same issue with my phone and it was definately CWM touch that messed it up . Samsung has a one year warranty on these phones.....and even though mine was bought as soon as they were available which was last june I called samsung and was told my phone is indeed under warranty until december of this year by it`s lot number...so as you can imagine I am sending mine directly to sammy free shipping out and back She expected to have my phone back to me in five to seven days !!! Samsung support number 1-800-726-7864 Hope this helps !!!
With that said I'm not going to state the ROM flashing experience is to blame here as it would be highly unlikely but at the same time I have seen very odd things happen such as ROM's causing documented digitizer problems on the HD2 when Android or Windows Phone 7 are installed. A while back on the I9000M platform a leaked firmware was causing similar issues to the oneNAND and it was documented as true hardware failure as I could never pull one out of it's partition problems either