If you are using an instrument (or miles), anything available in R will clear instantly.

Not sure how agents see it on their screen, but if it involves a connection, assuming the flights are on a through fare (same fare class on both flights, as opposed to say, one in W and the other in V), UA.com at least will only show the lowest number available on either flight. If their screen looks the same way, then perhaps that could have been an issue. Clearing is based on the availability on an individual flight.

Example, flying DAY-ORD-PEK. DAY-ORD on an individual basis is F4, RO, while ORD-PEK is F9 R2. If you look up DAY-PEK, and its a through fare, this connection will show both segments as F4 R0. However, if you were to apply a GPU, it would clear onto the PEK flight, since it basis it on individual availability. UA.com at least, was purposely programmed this way.