The passage Rock quoted tells you that if you're keeping mirc.ini in the same folder with mirc.exe, you don't need the -r switch. The scripts are "remembered" by being in the [rfiles] section of mirc.ini, so if your mirc.ini is getting trashed and then re-created the next time mIRC starts, then that's why scripts would become unloaded. When mirc.ini gets recreated, it goes back to the default filenames for variables storage, so if you're not keeping variables in the place where mIRC looks, ie vars.ini, they will appear to disappear.
As for why mirc.ini disappears on you, i dunno. I've had encounters with quite a few users who've had mirc.ini get zapped, but that usually happened intermittently when their pc happened to crash while mirc.ini was being written to. I haven't verified this is still happening to them with newer mIRC versions, and none of them was having mirc.ini consistently disappearing on them.
