Oh, okay. I verified the disk, then ran maintenance, cleaning and automation. Mostly I just have it clean up temporary files, caches, etc. I can't tell you each and every thing it does because there are a lot of check boxes and I don't use all of them. Running it a second time really seemed to do the trick, though.
Because inquiring minds want to know, which of Onyx's many tasks did you run? Simply saying that you "ran Onyx" doesn't give us much information.