Those are variables that represent other sources of code. I'll briefly touch on each of the different kinds of variables and where you can edit them from:
1) %%LNG variables are Language Variables. They are set from the language.ini files located at /language/[yourlanguage]/
2) %%Panel variables are Panel Variables for including Panels in the /templates/[yourtemplate]/Panels directory.
So...for example. %%Panel.AccountOrderStatus%% (as seen in account_orderstatus.html) would be including the file located at /Panels/AccountOrderStatus.html.
3) %%Snippet variables follow the same format, except the files are located in the Snippets directory of your template.
4) %%GLOBAL variables are Global Variables. They are set up from several locations, but usually from a file located in the [cartlocation]/includes/classes folder or the [cartlocation/includes/display folder. They will be set up from a PHP file, though, so that should help some in tracking it down.

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