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.
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.