I know what you're going through, just spent over a month of the same problems with the X4, got the same story, it worked on our 04 PCM, it recognizes other Ford vehicles. I went as far as buying a second one, getting my PCM reflashed, shipping the first one back twice, over $900. Not so much as any kind of an offer to make some of it right.
Vivian got involved because I had bought the Looney and a Tow from them and had her rewrite them for the second X4, which didn't recognize my vehicle after updating either.
After around 200 03-04 6.0's later, OH!! Maybe there is a problem, took them 4-5 days and they got it fixed and are busy getting the others updated.
Yup, know how you feel, makes me want to stay away from any updates, If I hadn't bought the second X4, I prolly would have picked up a NIB X3 that a guy offered.
Now I have a spare X4 for sale. Analog Gauges!!& ScanGaugeII.
04.5 F-350 KR. UCF Heads, ARP Studs, 6.4 Pushrods, KC Stage 2,SCT X4, BPD Air-Oil Cooler w/Bypass Filter, EGR delete, Coolant Filter, 4" Flow-Master exhaust,AEM Brute Force HD Intake, Atlas40 FICM, DC Power 190,BPD Scan-Gauge II, EGT/Boost/Fuel Gauges,Front Level Kit, PowerStop Front Brakes, Sinister Y-Pipes & R.R Fuel System,BPD Billet Wtr. Pump, '97 Fan Clutch/ BPD Adapter. WPE White Rain,W.Street,W.Tow, TSD-SPD. Riffraff boots, Cold Side Pipe.