sound's altered when controlling my Indigo via Midi...

[Origami]

I'll try to explain my problem briefly.
I bought an Indigo months ago but haven't had much time these months and I'm a newbie regarding harwdware synths, so my learning curve with my Virus Indigo is slow.

well, my problem.

When I control my Virus Indigo via Midi, in FL Studio or Sonar for example, the sound is altered; sometimes almost imperceptible, sometimes slightly, sometimes dramatically. I don't know what's the cause of the problem. I have Local off selected, and Midi Panel as Int+Midi, and also tried Midi alone.
But same problem.

For example, I was playing a melody this morning using patch c12 called Basstard, and when I played my Virus alone it sounds good, but when I control it via Midi with the sequencers, the sound changes a lot, it gets a strange flangerish effect and I don't know why.

can someone help me? thanks in advance