Not a problem that I have encountered so I'm not sure what to do to rectify it, but as a
potential aid, which Cubase are using and does it do this everytime you record? It may be
worth checking some of the options under the transport section as this can cause some
unexpected behaviour, but usually pre-roll or punch in matters.
I take it that
it is still recording the audio, but just off setting it to where it should be?
It might be worthwhile re-installing or trashing the preferences, but don't rush to do
that as it may be a simpler issue.