Files opened via the flipbook thumbnails, always load direclty the bottom layer as the active layer, not last layer active while file saved ; it's visible working with *.ora or *.kra who both format save the last layer used ( active layer ) . 

To test : 
1) Download : http://david.revoy.free.fr/forums/krita/2013-01-19_layer-active.kra.tar.gz
( Its a series of 4 *.kra files , similar aspect thumbnails )
2) open the four file independantly in Krita, and check : first file have first layer selected / second file second layer ... etc.... etc...  The layer are named also to give feedback on the active one. 
3) Create a flipbook with the 4 files
4) switch between the 4 files using flipbook thumbnails : only bottom layer is selected ; and it should select the last active layer. This is a workflow breaker.