Ok this may or may not help, because there are a couple of big differences in my setup:
(a) I don't have a Virus currently so I'm using my Ultranova which it's own VST and USB integration similar to the TI series
(b) I'm using Cubase 7.5 and I'm not sure if parts of what I'm about to write are the same in 6.0 but hopefully the principles still apply
My Cubase template project for the Ultranova has two tracks that apply to that hardware synth -- one for the MIDI and one for the audio output. It's been a while since I set it up that way so I don't remember all the reasons why, but I seem to recall doing that because if not the Nova output would go straight to stereo out, removing a lot of mixer flexibility. If your setup is not like this, you might consider going this route. If I wanted to I can just capture the output from the Nova on that track, working with it independently from the MIDI data and the Nova, which comes in handy anyway since it isn't a multi-timbral synth (the Virus of course is but there are times when the DSP power might nag at you to work with only one patch at a time anyway). So it's bounced to audio at that point but it's not necessarily a final commitment to that audio take as long as you can get back to the same patch on the Nova if you need to modify and record again.
But if I am sure I only want one sound out of the Nova for a track, I can leave audio capturing out of the picture as long as I do a real-time mix down, and that's the key setting in the export dialog that I think is your best hope. If it's not captured in a real-time mix down the synth DSP probably can't keep up and produce the audio efficiently enough to meet the demand of the DAW. So if I exported batch channels without ticking the realtime box, I've got nothing from the Nova on any wav files that were created. In a realtime export I've got audio from the Nova on both the files produced from Stereo Out and from the track handling the Nova audio output (even though it was never captured as part of the project), and of course in either case the MIDI track that the Nova VST is on produces no sound at all.
Something slightly different is going on with your setup and I'm not sure if that's your version of Cubase or the way VC does things, but the fact that you are able to mix down a smaller clip of the track and not the whole thing leads me to believe doing a "safer" type of export (namely real-time) would address any DSP bottlenecking. Just small things like reverb tails, envelope release values and of course total keys played could make a big difference in whether a non-realtime export would work in one portion of the track versus the entire track.
Sorry if it's old news but I couldn't see that you had tried this or thought of it from your post.
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