You are probably missing routes as the Airnav server is still likely to be struggling a bit at present, if you don't have the routes in your database the lookups may not succeed.
As for flight IDs, you receive them direct from the aircraft so if you have a slightly poor path and some transmissions are not received then that could explain it.
Can you determine whether there is a pattern to it, i.e. more distant aircraft tend to have fewer flight IDs received?
