By accident I described a related problem in an other thread (if interested se
Musical Mode vs Linear - Cubase - Steinberg Forums) but vic_france guided me to this topic, which seems more relevant.
The problem seems to be related to how Cubase handles the start point of a clip when pre-recording is on.
A workaround could be to go into Preferences>Audio and set “Audio Pre-Record Seconds” to 0 (if you dare! next time you record you should be absolutely sure when to pres the record button 
)