Possibly a near dead lnbf. Did this just start or has it always been this way from
installation? How long has the system been up? How old is the lnbf? Do you have any spare equipment you could start replacing items with to see when it goes away? My first thought was wind and a moving mount but you stated that is not a problem. Is it consistant? Sometime you will lose signal due to issues on the other end. A bad storm at the uplink location can cause it as an example.
Do you have the problem when the receiver is out at the dish on a short piece of coax?