Gedit's LaTeX plugin opens a dialog called "Choose Master Document" each time a .tex file is opened
The LaTeX plugin creates a hidden file .NAME.properties.xml (where NAME ist replaced by your .tex file's name) in the same folder as your .tex file. This file contains the settings for the master document, and if it's found the plugin doesn't ask for a master document.
A sample file looks like this:
<?xml version="1.0" ?><properties><property key="MasterFilename" value="my_master_document.tex"/></properties>
There doesn't seem to be a way to switch of this behaviour.