When using VST instruments along with effects in cubase, a delay will sometimes be introduced (this applies especially to dynamic processing effects such as the compressors/limiters that come with cubase). This does not apply to audio channels however, so if sometimes things just dont seem right - its worth checking and mixing down the offending channels.
Also, never underestimate using mono samples. Only use stereo if you really needs it. Apart from the obvious file size reduction, mono can provide all kinds of advantages.... which I cant be bothered to go into now so just do it...