Refinerys work completly fine with RF just tested it and hooked up a few refinerys with some conduits from enderio and put some oil in (all workes like it always did)
maybe you inserted the oil in the wrong slot? you have to put the oil into the double tank -> the single tank is the output
maybe you inserted the oil in the wrong slot? you have to put the oil into the double tank -> the single tank is the output