I also guess it's the fuse update, was hoping that 2.9.6 will fix it again,but doesn't look that way.
On Mission 13 non of the Bombs worked for me, just the Rockets were fine...
Problem with the Mk-20 Rockeye is also that since the update, there is no Fuze with an Height release for the Bomblets, only a fixed time. Maybe it makes sense to switch to CBU 99 in all missions.