dtboos
Robert,
 
That sounds good.  I'll be figuring out which one(s) are the culprits and keeping them out until the mixing/mastering process.  Appreciate all the help, I was panicking for awhile there.

You could list all of them here, likely some of us would be able to identify some of them.
 
Bob Bone
 

I knew the answer from the post title. Glad Bob pointed it out immediately. 
Until you learn the bypass trick there is very few systems that will not have latency of this type. The look ahead processors are the main offenders. But if you read up on this issue you might learn that there is a tiny little bit of latency added from even a simple reverb plug in. So you may not notice but it apparently can mess up Sonars ability to adjust for latency and your audio track may be recorded off time. Of course midi does not matter as you can quantize and it will be bang on. But careful with audio recording while using too may plug ins. To be safe, I always bypass all bins. There's a little icon for it in the tool bar. 
 
 

If you want to hear your full mix when tracking, bounce the mix to a new track in the project, call it "tracking mix" or whatever and output to main out.  When recording, bypass all the fx, then solo this and the track you are recording on and you can have the benefit of playing to the full mix with no latency.

Interesting thread.  I am having some weird latency problems as well - all of a sudden for some reason and I have not changed any sounds, VSTs, settings, nothing since the last time I worked on this file.  Running a Win 7 machine with tons of power, RAM, etc.  Interface is a PreSonus Firewire unit I have been using for about a year with no issues. Problems first arose with a previously recorded track using the Rolan TTS-1 VST.  When played the track today some of the notes were not playing... I can see the notes in the piano role and can manually trigger them with sound, but they do not trigger when played in the track.  If I move the silent notes a bit to the left they play, but then other notes do not play.  After failing to diagnose things I tried to just re-record the track and noticed that synth had some latency that wa not there before.  Checked my settings and tried to play with the buffer, rate, etc, but the bit rate and buffer settings are grayed out and I cannot adjust them.  Interesting thing is that when I close the settings windo, after changing nothing, the latency is resolved, but then returns when I play the track or try to record.  Not sure if these two issues are related or coincidence, but not concerned about the lack of settings access.  Is that normal when using a Presonus or Firewire ?  Does the PreSonus override the settings somehow ?  If so how can I fix the latency issue.

Set ASIO to a low number in Preferences while tracking and a high number while mixing.

Dropped MIDI notes usually indicates too small a "Prepare Using nnn Millisecond Buffers" setting in Preferences > MIDI > Playback and Recording. Try increasing the value from 250 to 500 or 750

Nice call scook !  Bumping to 500 solved things.  You guys are great, can't believe I got 2 responses and a solution within 3 minutes, awesome.
 
BTW, anyone migrated from X2 or X3 to the Sonar Artist or Pro ?  Good thing ?  Worth it ? Your older song files playable and editable ?  Any snags m,igrating ?

Hi all.  I'm getting a similar latency issue now with vocals.  When I monitor the vocals they are in time, but once I start playback they are slightly delayed.  Cannot figure out what is wrong.  I'm running vocals through the same a PreSonus Firewire unit I have been using for about a year with no issues.  Vocals were fine until I adjusted the Midi Millisecond Buffers to 500 in Preferences > MIDI > Playback and Recording to resolve the previous VST instrument delay issue.  But my vocals have been set up as audio not Midi so not sure if that has any baring.  Appreciate some advice.

So my latency issues are back again.    Trying to lay down a bass track over top of a bunch of existing tracks (all bounced clips) using a VST (SI Bass Guitar set up as a basic Instrument track).  When I first play some notes on the new track they sound fine, but as soon as I play along with the other tracks, the new track gets some latency.  Played with the buffers, but no luck.  Trying to "set ASIO to a low number in Preferences while tracking and a high number while mixing" per konradh but can't find where to do that in the ASIO panel... can someone guide me to it 
 

Are you using any plug-ins with look-ahead, maximizers or transient shapers?