I typically use an alias from Terminal.app to start SLT. I've started it a handful of times now, with an argument of the folder I want to edit. Looks like each time I do, a duplicate copy of the folder gets added to the project. Goto Anything then indexes all the files in that directory many times, which pollutes the results.
Quitting out of SLT and restarting it remembers the folder list. The only way I've found of fixing this is to Remove All Folders from the project and start again.
I'd suggest making it so the same folder can't be added to the project more than once. Also, it might be worth adding a config option for whether SLT remembers the project between sessions.