doesn't obey user.js? setting custom proxy settings

I'm not sure if this is a bug or just misconfiguration:

https://trac.torproject.org/projects/tor/wiki/doc/TorBOX/Dev/ClientVM#IcantfigureouthowtopreconfigureTBBtousesocksport9100

I set socks proxy to a non-default value. Either it ignores that and uses 9050 or it sets and empty values. In this case, behind a transparent proxy TBB will continue to work but show that scary red X icon.

Setting cusom proxy through gui works, changing the IP from localhost works. It's only the Port that is showing these problems.