Ok, so the problem is the following:

I shut down my PC while mIRC was running, using the power switch (due to a game freezing the computer).

I rebooted and started up mIRC again, and now it had "forgotten" the files which are supposed to be loaded on start (scripts, variables, userlist, etc).

While this behaviour isn't common at all (happened to two times in ~5 years), is there a way to ensure that mIRC remembers the files to load, regardless of the way it exited? Note that this isn't a 6.17 specific problem.

I would say try loading your scripts, shut down mIRC,
then open mIRC again, could be worth a shot imo. It
seems to me that variables behave the same way, any
variables that are set are not saved to file until mIRC
exits clean, and yes it's annoying as hell on the rare
occasion that it happens to me, which is pretty much
only due to power failures.

~ Edit ~
Then again there is the /saveini command.

Try seeing if one og the INI files is read only.

You can always try using FlashINI command to save the changes into the ini files while mIRC is still working.

What is the FlashINI command?

It is a flushini with typing mistake :

/flushini <filename>
Flushes the specified INI file to the hard disk. INI files are cached in memory, so you may want to do this to make sure that your INI is updated properly.