I deem Necrotherion's case could have another reason. A rebellion of this extent is unlikely to be caused by 'regular' loyalty issues, it isn't too probable that all provinces start rebelling and all wiped-out factions re-emerge the same turn just because loyalty was below 120% (and still in the greens).

To me, it seems more likely that the cardinal sin with large empires has been committed here - namely, attacking with or isolating the Emperor. IIRC an attack may result in him being considered 'cut off' for a short span of time during two turns, usually enough to trigger rebellions in a large empire. As Innocentius has mentioned, the HRE additionally seems to be particularly weak in this respect.