Considering how old mIRC 6.31 is, it wouldn't surprise me a bit if there were issues. My suggestion is that you download and install a copy of the most recent version from [url=http://www.mirc.com/get.html[http://www.mirc.com/get.html[/url]
I also suggest that you remove the multiple copies of your custom remote.ini, and keep a copy in a safe external location.
Then install mIRC, and then copy your custom remote.ini over the one that is installed by default.
After doing that, you should be able to run the most recent version of mIRC with your custom remote.ini
RE: Loading Popups.ini, this file has to be loaded several times for the whole thing to be loaded correctly. There are 5 different areas where it has to be loaded.
To simplify, the loading you can use
/load -ps popups.ini
/load -pc popups.ini
/load -pq popups.ini
/load -pn popups.ini
/load -pm popups.ini