Some questions:
(1) So you switch sessions, giving you the new underlay graph. Then you manually use Dataset#N to select the new overlay dataset to graph. That works through several session changes, but then goes bad?
(2) And if you then manually interchange their roles (via the 'Overlay' and Dataset#N controls), things are cool?
(3) And if you manually switch back to the way you want it -- that restores the problem or things are OK at that point?
Offhand, I'd guess that something to do with the automatic directory rescan is happening, but that's just a wild surmise on a peak in Darien.