'Custom script' is a scripting language known as Jass; when the editor compiles a map being saved, all of your triggers are converted to jass and assembled into a single file of text. You can write jass directly by creating a trigger, selecting it, going to the edit menu, and selecting 'convert to custom text.'
Most Jassers these days have also adopted a bunch of extra formatting/syntax options known collectively as 'vJass,' which require a special jass compiler which doesn't come with the normal wc3 editor so that you can save maps using vJass. A version of the wc3 editor with a vJass-capable compiler can be downloaded here, or on the same site you can find the Jass New Gen Pack, which combines this and many other features.
A ton of jass tutorials exist, but I recommend you start here once you have one of the aforementioned world editor programs up and running.
Ghan has said he has fixed this. Monovertex please confirm this fix. This was only a problem with people that had signatures in the upper levels like not the special members but the respected members.