Summer-16 release notes:

Actually with summer-16 they have improved the cross-namespaced limits.

but the Limits that are shared across all namespaces, such as the limit on maximum CPU time, remain the same. The new cumulative limit doesn’t affect these limits.

I don't think there is any direct reason or change which can start causing the CPU timeout exception.Maybe you can provide detail of supporting code sample etc maybe that is helpful

Summer-16 release notes:

Actually with summer-16 they have improved the other cross-namespaced limits.

but the Limits that are shared across all namespaces, such as the limit on maximum CPU time, remain the same. The new cumulative limit doesn’t affect these limits.

I don't think there is any direct reason or change which can start causing the CPU timeout exception.Maybe you can provide detail of supporting code sample etc maybe that is helpful