When you manually edit mirc.ini mIRC will just remove all changes, but if you $compress() the file then many of your options will mess up as mIRC doesn't remove some of the compressed data from the top of the file.
Some of my options were left intact, but most font and size options were lost (Font in status/channel/query/script editor wasn't the normal font, script editor size wasn't the normal size).

I realise you shouldn't use $compress on mirc.ini but since mIRC automatically fixes the ini file if you edit it i'd expect mIRC to fix it when you $compress the file as well.

It was compressed with the l6 parameter in case anyone wants to try and reproduce this.