You say the in points are wrong. Is every clip wrong? How far off are they? Where did the quicktimes come from? Were the quicktimes made with a hardware decoder during shooting, or made afterwards from the R3d files, or are they the mov proxies accompanying thr R3ds. Is that a consistant number of frames or is it random?
Sounds like the mov files have different timecode than the R3d, or that the wrong embedded timecode or edgecode or absolute or camera tc box in the R3d raw options is checked.