Imagine the following situation: you're on 2 networks and 2 channels with the same name. Let's call the channel '#Test'.
When disabling Logging for #Test on one network via the System menu, the other network still continues to log #Test correctly, so far so good.
The problem begins when having shutdown mIRC and starting it again: now the channel #Test on *both* networks have logging disabled, while the other one should still have Logging enabled.
Looking in mirc.ini the reason becomes clear why this behavior occurs, under [logging] it is only saving
instead of for example
So, at startup mIRC cannot determine what network to disable logging for and so disables it for all channels with the same name across all networks.