It reminds me about his issue
from Reporting a changed latency in VST plug-ins - #12 by ckk
One, in particular, was quite annoying: when loading a session in Cubase where the plug-in state implied a latency different from the one of the plug-in in its “just inserted” state, the whole session didn’t output any sound when played even if the meters in the GUI moved as if playing was actually happening.
If its this issue, it looks like a bug in Cubase, somebody should contact Steinberg.
But anyway, i would recommend to set the latency as early as possible (in prepareToPlay or setStateInformation() your plugin should at least know its latency?) or later when the user changes the latency setting from the plugin-GUI.
BTW: could be of course some other issue too