I had my Portal 2 challange rejected for some reason. I synced my trophies before I submited. Better try again and submit the Steam achievement one as well just to be safe.
What do you use to submit PS3 trophies now? Because from what I understand you need to use a third party site or take a photo to submit. I used to use yourgamercards.net but that site seemed to have disabled searches for PSN ID's and is only generating a gamercard to url link.