Yes. I was on my mIRC today.. and for some reason people cept noticing me to Respond in PMs. I noticed the people back telling them I have not recieved any PMs from them. I thought of my script for the first thing, but nothing. I turned remotes off, and used /! in all my commands I made. Nothing still didn't worked.
So I checked in the mIRC Options for anything to block the Query Windows from showing.. Nothing that I can find.
I also doubled check. "+m" is not on. only user modes are +xnR.

Check options/other/lock to see if you have disabled "private chats" as that includes query as well as dcc chat.

Is it possible one of your scripts put them on ignore?

Not knowing what network you frequent, i dont know what the modes xnR are for. R could be restricting msgs to you only from registered and indentified nicks.