I realize this is an old thread, but I am seeing this same thing, and I'm not sure that there was ever a really satisfactory answer above.
Until now, I have just set up "simple instrument" tracks (or used audio that was recorded on an external device and imported into SONAR). Although the simple instrument tracks have MIDI, I believe the meters show only the rendered audio returned from the soft synth. So I never saw this "clipping" before -- except when I was really clipping, of course.
The past few days, I have been working up the learning curve setting up routing for synths that can do multiple channels (TTS, Aria, Session Drummer, etc.) And now that I have MIDI tracks separate from the synths, I am seeing those clipping indicators light up on the MIDI tracks, just as described above in this thread. I don't hear any clipping and the audio tracks all look OK.
But I don't really think it is acceptable (as a long-term thing) to say "just ignore them". Clipping lights should not be showing if there is no real clipping. I don't want to start another cycle of flame throwing, but it really would be nice to know if this has been accepted as a bug. If not, I'd be happy to write up a bug report.
I am really wondering if those lights are actually intended to have a different meaning for MIDI tracks. After all, the green "LEDs" don't ever max out, so it makes no sense for the "clipping" indicators to light up.
While on the subject, can I get some advice about using the MIDI tracks? My intention is to have one audio track for each MIDI track (or possibly multiple audio tracks for one MIDI track in the case of drums.) That being the case, it seems to me that I should plan to do all the volume, panning, and FX on the audio tracks. In other words, I should set the MIDI fader at unity and dead center on the pan. And I should not mess with any mixer settings inside the synth VSTs. Is that what y'all would consider best practices?