There's actually only 900 crates + 10 golden ones, count being 1000. The screenshots with 1009 and 1051 crates are taken from the Garry's Mod version, not the HL2 mod.
Be sure that none of the crates is jamming the conveyor belt at any point. I think I had this issue as well at the beginning, but if it wasn't for the jamming, I don't remember the cause for it.