It is not possible for only some of the data in the tun file to be programmed into the PCM. Either it all goes in correctly or the PCM will not operate. The engine would certainly never start if even just one byte was missing or damaged.
So you really need to look at what the data is that you're programming into the PCM. What has changed in the tune since the fans were working correctly?
Do you still have the *.tun file that was in the PCM when the fans were working correctly? If so try that.
Just to prove to yourself that all the data is programmed correctly then, as Joe suggested, read out what is in the PCM and compare it to the file that you most recently flashed into it you will see that they are identical.
Regards
Paul