ReCore and FlexX/-SIS in GUI modes (Release 3.1 and newer) may crash with some input molecules. All of the problems like this could be resolved so far by updating graphics card drivers.
Vista provides an automatic way of doing this; here is the procedure to follow:
1) right click on desktop - hit Personalize
2) New Windows appears: Control panel personalization
3) Click Display Settings
4) New Window appears -> hit Advanced Settings button