I pasted 500 random lines of stuff into the theme.mrc and it saved fine, but not my theme which i i cut and paste from a text file.
This is why I suspect Anti-Virus software might be the cause. I'm sure in the past AV software has actually determined specific mIRC scripts to be viruses and, with the crappy state of AV software, it's quite possible it's preventing mIRC writing/reading the ini file without even telling you what it's doing.
