In my prefs, I have “stop playback when winding” unchecked.
Sometimes (quite often) when I FF/RW Nuendo keeps on playing back the audio where my cursor was for quite some time before actually switching to playing back the audio where I wound up.
I discovered that when N6 is hooked up via MMC and TC (ie running as a slave in effect), when pressing stop, sound continues for some time afterwards.
I looked (by some weird instinct) at the ASIO protect status. I switched ASIO protect OFF and the problem has gone away.
This may be related to your issue.
I later checked and saw that the disk pre-load buffer size seemed to match the “delay before silence at stop issue” that I was experiencing with ASIO Protect on.