I have heard that the browser needs to be reconfigured if you are going to use the system daemon to send all of the machine’s traffic to the Tor network. Maybe in your case you need to do the same thing.
I’m not sure how to do it right, so check out this thread and look into tor-browser_en/Browser/start-tor-browser Where you will find
# Additionally, if using a system-installed Tor, the following about:config
# options should be set (values in <> mean they are the value taken from your
# torrc):
#
# SETTING NAME VALUE
# network.security.ports.banned [...],<SocksPort>,<ControlPort>
# network.proxy.socks 127.0.0.1
# network.proxy.socks_port <SocksPort>
# extensions.torbutton.inserted_button true
# extensions.torbutton.launch_warning false
# extensions.torbutton.loglevel 2
# extensions.torbutton.logmethod 0
# extensions.torlauncher.control_port <ControlPort>
# extensions.torlauncher.loglevel 2
# extensions.torlauncher.logmethod 0
# extensions.torlauncher.prompt_at_startup false
# extensions.torlauncher.start_tor false
#
# where the '[...]' in the banned_ports option means "leave anything that was
# already in the preference alone, just append the things specified after it".
Sorry, I forgot to add the link.