Save and restore default buttons
It is important to realize the the Time Lord Graph Selected Methods listbox has its own Save button just below the two arrow buttons sandwiched between the Available Methods listbox and the Selected Methods listbox. Clicking the Save button at the bottom of this window will not save the Time Lord Graph Seletected Methods settings. Once you have the Selected Methods set up the way you want click this button:
The Restore button is immediately below this one and will restore the last saved Selected Methods configuration.