That's not correct!
An 9600 phone (9620/30/40/50) will load 96xxupgrade.txt first and then 46xxsettings.txt.
An 96x1 phone (9608/11/21/41) will load 96x1Hupgrade.txt first and then 46xxsettings.txt.
The upgrade files have this line, that tells the phone to load the settings file:
GET 46xxsettings.txt
So first is always the upgrade file. Check what IP Office shows you in this file. As 9600 phones are EoL (or only EoS - not sure) it seems that the autogenerated file doesn't contain any information about firmware update files:
## IPOFFICE/11.1.3.2.0 build 6 192.168.x.y AUTOGENERATED
IF $SIG SEQ 2 GOTO SIPUPGRADE96XX
GOTO GETSET
# SIPUPGRADE96XX
GET 96xxupgradeSIP.txt
GOTO END
# GETSET
GET 46xxsettings.txt
# END
If so, you have to upload a valid upgrade file yourself.