I don't think so.
I test again with no script and aliases, the situation still happens.
After I re-logging (stop logging and enable it, choosing the same directory and file), the mirc.ini changes as follows:
Before:
[logging]
#channel=#channel.log
After:
[logging]
#channel=logs\#channel.log
I think that the logging folder in Alt+O->IRC->Logging does not work in individual logging.
And the session restart problem still exists when disconnect.
The current session stores in #channel.1.log and insert to #channel.log after session close. I don't know it is a bug or a new feature. I prefer the old one.
