I have this problem when I germinate as well.
I have not found the problem or the answer for it though I think it's a soil problem.
Right now I have a BBK and ABB that both had this problem when starting, the BBK cotyledons were almost fully yellow/brown. I also had to pull the slimey goo off my sprouted seeds.
This yellowing caused my BBK to be 2 weeks behind.
When this happens the plant takes longer to start growing and I notice the plant stays "white/yellow" for a day or 2 before it starts turning green, when a normal seed with no problems sprouts I normally see it turn fully green from white in 12 hours or less.