I have noticed the same thing and it is a pain!
I can not see my January flight DCA/SJU/EIS on the JB website.

If you select the Jet Blue using KAYAK it will take you to the Jet Blue site where you can book the flight.
JB told me this has something to do with the code share flight on Silver.

Also, once you book the flight, you can not use Jet Blues "Manage Flight" option to view or change seats etc.

JB also blamed the Silver code share connection for this as well.
Any changes to reservation have to be done by calling Jet Blue.

I have never had this issue with United or AA code share flights.