I also found this problem of HJG aeroplanes not showing up in my most recent FSX installation after carefully following all instructions and previous installation success in another computer.
I am running FSX SE now and what fixed it for me is:
Change all texture entries in the aircraft.cfg from [fltsim.00] ... 01 ... 02..... to [fltsim.0] ... .1 ... .2
So, remove the first 0 for each entry.
Also make sure that the entry following "sim=" matches the name for the ".air" file exactly.