Nuendo is exporting audio late.

[stingray]

Never seen this here. IMO most likely cause would be a plug-in.
Do you ever get the same thing happen if you simply export the audio from a VERY simple project? Such as, one short audio file on one track with no plug-ins at all in the project.

Also:
What is the bit depth / sample rate of your projects?
What is the bit depth / sample rate of the export files?
You say you de-activate plug-ins on the master bus. Do you have plug-ins on the other audio channels of the projects where you encounter this problem?