We had the same situation, I was able to flash the custom rom but not stock. I flashed the 4.4.4 stock rom and I tried to boot but a screen occured than I flashed the 5.0 rom and my phone booted up.
I assume that this issue is caused by wiped TA partition after bootloader unlocking.
With my best knowledge, some of customized official ftf has blank TA partition or no partitioning in its ftf.
I found
this last night, and I could get my Xperia Z recognized on the Emma, and flashed with geniune service port. (it shows the right one automatically)
But the issue has remained yet. My device is being recognized only as some weird name of device under Emma (I guess it's following the information based on the IMEI number)
anyway, I guess I may give up at this moment... I can still flash and use with AOSP based ones...