EDIT: Before all that stuff below, try setting the program to just encode, not encode and decode. The radio may not like the tone squelch combo, even though its a programing option.
That's odd. Its been a long time since I have used one. I may be thinking of another model, but IIRC, TA is something that typically has to be manually selected and it is selected on the per group basis. If you press and hold the the AUX button (or scan. don't remember), and then power on the unit, that puts the radio in FPP mode. From there you can scan through the menu options to enable or disable TA on a specific group.
If that doesn't help, I would see if you can find someone with a working radio and clone their unit to yours. From there, make a backup copy on your computer and then try to mod the image again.
Also, what version of Windows are you using? That software was created for DOS and DOS hasn't existed since 1995. If you have Windows 7 or older, you can make a dual-boot computer with DOS 6.0 or 6.1. The command prompt on anything newer than Windows 95a is not true DOS, but rather it emulates DOS. You may be having a timeout issue while programing it due to the emulator timing out. I have the same issue on one of my radios. If I upload the configs once, it fails to set everything. However, if I upload it 2 or 3 times back to back, it works fine.
The reasoning behind it is the radio is taking to long to send the kill command, indicating to the software that the programing is done, so the software times out. When you do multiple writes, one after the other, the second and third attempts don't have to do anything but verify the settings are already present. If no change is needed, it keeps going and eventually finishes. The only caveat is, you have to keep it in the programing mode. If you reset the radio and then try to flash it again, its the same as starting from scratch, and it won't work.
I am a computer systems engineer with over 30 years of experience. I have been specializing in Microsoft operating systems since 1991. To this day, I have not figured out how to change the TTL in the CMD DOS emulator... so I just put up with it.
I hope this helps. If it doesn't, I hope someone is able to get you the support you need. Looking forward to your follow-up. Good luck!