I think (!) that the GW platforms at Oxford are arranged such that Northbound is 'Down', Southbound is 'UP. However, the "new" line to Bicester (and thence to London) is Northbound (Bicester-wards) is 'Up' and the Southbound (to Oxford bufferstop platforms) is 'Down'. If so, then platforms 1 and 2 have the opposite sense to platforms 3 and 4. Am I right? If so, then the 'up-down' thing could be hugely confusing.
I'm not sure if I'm understanding you entirely correctly–this is the sort of thing much better suited to diagrams than words–but that doesn't sound quite right to me. As I understand it (and happy to be correctly by those with more local knowledge!):
The directions change at Gavray Junction where the Down Bicester South West Chord branches off the Up Bletchley and the Up Bicester South West Chord comes off the Down Bletchley.
Or to put it another way, trains from Bicester heading towards Oxford will travel "down" until they get to Gavray Junction where they begin to travel "up."
Neither platform 1 or 2 is really up or down, although they're both bay platforms on the "up side". Of course what goes in must come out so they're used equally in both directions.
It makes a lot more sense when I see it drawn out diagramatically–I think, I hope I've got it right anyway. Worth a few minutes spent looking at the Sectional Appendix (although it is split over the GW and LNW(S) parts).