Hard to troubleshoot by mail, but the only significant thing I see from your replies is that it's not just query messages being blocked, but also notices, which means that probably /ctcp is blocked too.
https://freenode.net/kb/answer/usermodes shows 2 possible modes that can be on users which can affect this. +g blocks queries from other users until you accept them onto a list, but it should trigger a server message that so-and-so wants to message you, and you would've seen that. The +R keeps you blind to queries from those who haven't identified to services. Your user modes (not same as channel modes like +o for @op) show in your status window, and you can also see them from: //echo -a $usermode
When you send them to yourself, are they blocked too?
i.e. //query $me | msg $me test ... should show your message twice, once from what you type, and the other from the server sending it back to you
i.e. //notice $me test
or //ctcp $me version
You can test if your program got somehow corrupted during install, where this should say ok: //echo -a $file($mircexe).sig
You can come visit ##mirc at freenode and see if someone there has any other things to try
