After examining the file you sent me it appears that you have 3 FTDI based devices attached to your MAC. Two of them are Digilent devices and the third is using FT230X for the name in it's string descriptor. Both of the Digilent devices show that the Digilent KEXT is attached, while the other shows Apple USB serial. I thought that perhaps the Digilent driver wasn't attaching on your system but the log shows otherwise.
FTDI has their own kext that's supposed to prevent Apple's driver from attaching. It's called D2XXHelper. The downside to their kext is that it will prevent the Apple USB serial driver from attaching to all FTDI devices, not just the Digilent ones. So using D2XXHelper isn't a long term solution even if it solves the problem on your system. However, if you could try it out and let me know whether or not it addresses your issue I would really appreciate it.
I would detach all FTDI devices, run the pkg file, reboot, and then try attaching the Digilent devices again and run the digi_enum.py to see if all 4 methods of enumeration show the Digilent devices.
Do you know which piece of hardware the FT230X is associated with? The FTDI D2XX library will only allow a single application to open a device interface at any given time. If you are running any other software that opens FTDI devices with D2XX make sure that it's not opening the Digilent ones automatically otherwise that could lead to our software failing to open the device.
Also, to remove D2XX helper after you've tried this test you have to delete the associated kext from your /Library/Extensions directory and reboot.