I had a similar issue, not off by a few inches but noticeably off.. I updated my firmware on my FFD using an older version of flash print because the 2.xx version had a bug.. then you have to connect your ffd to you computer via usb to get it updated.
heres a cut and paste of the email I was sent..
"I want to say that you should update the firmware on the old software.
Please try to follow below to try again and check whether it works.
1. Uninstall 2.1 FlashPrint software from your computer.
2. Download 1.3 FlashPrint software from here:
https://www.dropbox.com/s/ngdmhjw59slkh ... 0.exe?dl=0
3. Install 1.3 FlashPrint on your computer.
4. Plug USB cable from computer to Dreamer. But do NOT power on the printer at the moment.
5. Open FlashPrint, go to menu "Tools---Update Firmware", a new window will pop up.
6. Select firmware: dreamer_2.0.20140827.bin.
7. This step is critical which concerns whether you can succeed uploading new firmware or not.
Switch on the printer, within fraction of second, click "Rescan" button on the new window in the FlashPrint, a new Serial Port will come out, select that port and quickly click "OK" button at the bottom of the window and then click OK in the popped up information window. Four actions: rescan, select new serial port and click OK button and click OK button again, must be completed within a very short time.
8. Process bar enable and new firmware uploading will succeed.
9. If the printer can start up normally which means new firmware has been uploaded successfully, then install the new FlashPrint_2.1.20140828 on your computer. You can connect the printer to computer via USB only using the new flashprint software. "
it worked for me both extruders find the middle of the print bed now.. even though Im currently using Simplify 3D