You're using tabs before the %, not spaces, right? Because that will align them but of course if you make changes to the length of the code line more than a tab, it will "jump" to the next tab. But at least they'll be aligned to the nearest tab column.
Make sure your preferences are not setup to insert spaces when you type a tab.
Home->Preferences->Editor/debugger->Tab-> Uncheck "Tab key inserts spaces".