When using the TextFX Tools sorting, Notepad++ will not remember the settings 'Sort Ascending' and 'Sort outputs only unique' the 1st time you click them. You need to click on then again to show a mark in front of them.
1) start Notepad++
2) go to menu TextFX -> TextFx Tools and clock on '+Sort Ascending'
a marking will show up in front of the menu item when you go to TextFX -> TextFX Tools
No marking is visible. When you click again on the menu item '+Sort Ascening', and you check it again, then you will see a marking in front of it.
The same thing applies to the 'ort outputs only unique' item.