Bah, ok thanks - as a workaround I just added a line to server.cfg so it would at least load on map change and server start-up.
Edit: Just went to check admin.sma as you said and I have found the line in the version that comes with 0.16. It's an easy edit of a single line that changes the path of amxx.cfg to execute so it is correct and in line with the rest of the AMXX configuration structure.
In admin.sma, on line 74 change:
server_cmd("exec addons/amxx/amx.cfg") // Execute main configuration file
server_cmd("exec addons/amxx/configs/amxx.cfg") // Execute main configuration file
Then just (re)compile the plugin like any other.
I'd just like to say that so far, I am very impressed with AMXX. It generally seems a lot nicer, especially the way in which the files are kept. Look forward to my donation in the future