Have you tried to switch off "ASIO Guard" in Cubase's Preferences?
/Dietz - Vienna Symphonic Library
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I run into the same problem at low latencies and/or as soon as I use more than four or five instances.
"Audio Input" into VE Pro has always been some kind of experimental feature. Most DAWs are not ready to send audio to an external application from anything else than their actual outputs; abusing a plug-in like VE Pro's "Audio Input" for this task comes for a price ... please keep in mind that VE Pro has been primarily invented to act as a MIDI host that reacts to incoming MIDI data, not audio.
Kind regards,
PS: This is the reason why the - actually stripped-down - plug-in version of MIR Pro has been invented at all. In this case, the hosting DAW is still processing the audio like with any other plug-in; it's "just" the GUI that runs in an independent process. No CPU-timing-critical stuff to compute here.
Good question! :-)
Back then, we were very proud to offer perfect alignment between Main Mic and the direct signal from virtual spot mic (i.e. MIR's "dry" signal component). As a matter of fact, we carefully cut any remnant of the recorded direct signal from all IRs and replace it in real-time with the readily positioned dry signal, to avoid any hint of phasing and/or timing issues. So there's nothing you could compensate. :-)
That said, I know very well that sometimes the delay between spot mic and main mic adds to the sense of perceived depth and enveloping. You can achieve this (in VE Pro only!) by splitting the wet from the dry MIR signal and adding some milliseconds of delay to the former.
HTH,
Yet another PS:
You might have seen the "Delay" parameter in MIR Pro's Output Format editor (which controls the Ambisonic decoder and contains the output matrix). Here you can add delay to individual virtual microphone capsules, but of course this will affect _all_ decoded signals then, so that's not what you were asking for.
... the main idea of this feature was to fine-tune the delay of microphones routed to surround channels.
Kind regards,