I’ve not had your exact problem, but there is definitely something flaky with exporting mixes in 6.5.
One track I’m working on garbles the audio on a vocal track when you export the full mix. It plays back perfectly, but when you export it, on 3 out of 4 bounces the audio gets screwed at the exact same point.
On another track, every track has been frozen prior to archiving - so no plugs / vst’s etc playing back, just plain audio files. It plays back perfectly, but when I export the mix, a group track cuts out half way through - I can’t export a complete mix without unfreezing the parts.
On another track I’ve got garbled static from a frozen bass part embedded in the frozen audio of a drum track!
I’m also going to try 6.5.1 even though it supposedly only fixes a score issue. In all my years of using Cubase there has never been an issue with exporting mixes till now on this latest version.