My guess is that both your issues have the same source. Its files created through Offline Prozessing or also called Edit Files (Files in Edit Folder.)
The Waveform does not match the actual content.
I have experienced that on projects created in N7, then opened in N8. Deleting the peak files and restarting does not help. Its allways clips with edits (OfflineProzesses) where that happens. (Please check.)
No error appears about faulty re-linking or missing files. But the content is completely messed up.
I do not think it Mac/Pc. (We germans have the problem with öüä when changing platforms. But then you would get missing files as this files do not have the same file name anymore.
I do not think its PlugIn versions (handling Offling Prozesses on tracks is handling audio files. PlugIn version would only make a differnce if you would want to reopen and change an OffLine Prozess.
What happened in your case (my guess) is that processed and not processed audio files have been mixed up. Whenever we create a OffLine Prozess Nuendo renders a sound files and places it in the Edit Folder. This sound file has the same name as the not processed file. This works well as long as your track stays on the same system. It works well when you export tracks including audio (now Nuendo gives it a unique name). But when you export tracks without soundfiles, because your partner allready has all (lets say) production sound on his system and needs only the newly created files from you (audio files or edit files) you are bound to run into problems. As soon as you have to do any relinking of missing files you are lost. Nuendo will mix up Edit files with the non Prozessed files. It catches just what it gets first.
We had a workflow for it but its complicated. I did end up with the solution to allways delivere xml with all sound, even if it means sensless doubling up of audio files. (Drives are big, download speed is high…)
If you find out that my guess fits your problem please help and do a feature request for unique file names in Edit Folder (or a option to relink missing files with checking file lengh). We can use one every month. Its a thing we worry about since N2.
Thanks for bringing the issue up.