Are you shooting autofocus with central spot or is this happening with manual focus? I ask as a user of the 1DS3 with the 85f1.2 mk2 myself because my 85 won't autofocus correctly at all with my 1DS3, sometimes it gets it but most times not. The camera has been back to Canon and has been calibrated with that lens, however it still cannot be used with absolute confidence. Ignore all the feedback suggesting that the 85 is not sharp at full aperture because it is, unbelievably so, but manual focus is the only option, and even then on certain subjects it's a little hit and miss, however when right it's sharp as a tack....
The 50mm maybe a different kettle of fish, and is a lens i dearly wanted to buy but did not because of the focus shift issues at close range and also its average performance at wide open, which after all is the whole point of owning that lens. In the end i decided upon a Canon 50macro and a Zeiss ZF 50f1.4 with a Nikon to Canon adapter. Even though they are not that fast they can both be used near wide open with confidence and do not suffer with focus shifting upon stopping down, something to do with the Canon 50f1.2 and spherical aberations whilst not having floating elements for closeup, unlike the 85f1.2 which does.
Hope that helps even though it may not be an answer to your problem, if of course you are experiencing the problem with manual focus also then you may have a poor performing (calibrated) 85mm, as i tested 3 in store to get the one i own and it was better than the other 2 all manually focussed.
Lastly, again if manual focus is your preference you may wish to consider a matt screen, as a colleague of mine did recently with his 1DS for use with his Contax 85f1.4 and 135f2, both of which are now bang on almost every time at full opening which it was not with the original autofocus screen. If autofocus is your bag then all i can say is good luck, cos i don't think the camera can be relied upon with certain lenses at anything other than closeup where it's reliable, and crazily enough my 135f2 is perfect wide open in autofocus or manual so what gives?