And I'm not experienced with scripts. The only ones I have are rarely used and only for colorful chats.
Sounds like a script that could cause the problem. In order to color up your chat, the script needs to halt the original message, and display the message on it's own, which means the script governs where the messages appear, not mIRC.
Try to unload the script, or type "/remote off" to see if the problem still occurs. You can turn the scripts back on with "/remote on".