If you call an alias, mIRC will first see if such an alias is defined in your remotes/aliases. It doesn't matter which file. If you have a alias called /mytemp in every remote file you have, then only the one defined in the first file will be used. So if you have the alias defined only once, it will be executed when called no matter from where it's called.
If that's exactly the problem (defined several aliases in different files), then I'd suggest changing it - it's very bad practice to create several different commands by the same name.
Personally, I also strongly object to the creating of an alias that uses the same name as a default one. It's not that hard to add an extra letter, and it leaves the default command open for easy use. (and yes, I know you can override custom aliases by using a !)
