I'm guessing the old version of MP MarcusB is talking about was 0.1.2.0 - I don't think that version used the Microsoft Stream Buffer Engine (I remember that recordings were done in .mpg, rather than dvr-ms).
I've been searching around a little bit - seems as if MediaPortal has always recorded in DVR-MS (correct me if I'm wrong). But nevertheless, since MP uses MPEG2 now, recording one show into two files for the "overlapping time" should be possible...