(Running SV 1.6pre1 on Ubuntu 9.04 32-bit).
If I run a plugin that gives a time instants layer (e.g. note onset detection or beat tracking) and then delete this layer the audible clicks for the time instants can still be heard over the top of the audio file, even though the layer itself has vanished.
Furthermore, the audible clicks are still present even if I undo right back to before...
2009-06-25 09:37:25 UTC in Sonic Visualiser