Update:
Turning on Transmit MIDI Clock resolved the MIDI latency issue with the Fantom.
Removing UAD-1 card, plugins, and drivers resolved a lot of audio latency issues.
 
I've had this problem for a while and I'm wondering if there is a way to fix it. I have a Roland Fantom X6 synth that I use for some of my sounds. I also use it a lot when working parts out. The problem I'm having is that when I use it to record an audio track from a midi track, the recorded audio is almost a 16th note behind the beat at 128.
Routing: Sonar midi -> USB ->Fantom -> Audio Out -> Sonar
Is there a tweak in Sonar I can use to tell it to send midi out early for tracks that use the Fantom so the audio lines up when recorded? Is there any way I can get the midi and audio to match up or do I have to always tweak it manually after the fact? It appears to only happen with the hardware synth, all the soft synths work fine.

If you keep your audio latency low with an ASIO buffer of less than 256 samples (preferably 128 or less), the latency should not be noticeable on playback, and just noticeable but not bothersome when playing live. If necessary, you can set a Timing Offset (msec) value in Preferences > Audio Sync and Caching. A positive value will delay audio playback relative to MIDI going to hardware ports (softsynth MIDI tracks are handled like audio, and won't be affected) to bring them in sync. But this also affects MIDI placement in the timeline when recording from a keyboard, so you'll want to make sure you don't introduce a problem there.
 
As far as I'm concerned, using a Timing Offset should be a last resort if you can't get your external and internal audio synced up without it.
 
 

+1
 
Each system with have its own "happy medium" for performance. I threw in a "Tailoring DAW buffers" at the end of this post.

Figure out exactly how many samples behind it is, and enter that as a negative value in the Manual Offset box.
 
If you don't want to do that, just nudge the rendered track. The way I do this is to insert a MIDI note at the front of the track via the PRV, with grid snap enabled so the note falls exactly on a measure. When I later play back the synth to capture the audio (usually via S/PDIF), I'll have an audio event that I can line up precisely with the MIDI note. Then I slip-edit the audio clip to silence that sync note. 
 

Dave makes a good point that audio latency should be dialed in first with a Manual Offset in addition to the automatic compensation that SONAr does (not to be confused with Timing Offset that alters the relationship between MIDI and audio), either by re-recording an audio track to check sample alignment or by using a tool like the free CEntrance Latency Tester to measure the actual latency vs. the latency reported to SONAR by the audio driver. But that error is nothing like what the OP is reporting in this case - usually less than 44 samples = 1ms at 44kHz. Whereas a musical 16th is over 5500 samples at 120BPM.
 
But I would set the Manual Offset where it needs to be to compensate normal audio recording latency and do correction for MIDI transmission/response/sync issues by other means.
 
 
 
 

Thanks for all the info, I adjusted the Timing Offset to 97 ms and the recorded tracks line up now. One side effect is that now the keyboard is really behind the soft synths and audio during normal playback (auditioning midi parts etc). I have the buffer on my MOTU 424 card set to 1024 samples, if I set it lower, I get dropouts on projects with 16 or more bounced tracks even if I have all the midi sources archived. I have a really fast computer with a lot of memory and I've done everything in the book to optimize it for audio, theoretically I should never get dropouts even with super low latency, I don't understand what I'm missing here.
Another thing I've noticed is that there is a significant delay between the time you hit a key on a midi controller and the time a note sounds when using soft synths. It's so bad it makes using a midi controller impossible with soft synths, the work around I've been using is to compose the parts in the staff view and play them back to audition them.
Thanks for your help.

Hmmm... something not making sense, That big timing offset should be making audio from the keyboard earlier relative to soft synths and audio, which was the goal. If that's not improved, what is? In any case, that big Manual Offset is going to cause all kinds of weirdness in different scenarios so you;re not going to want to leave it that way. It was meant to deal with the usual MIDI-Audio offsets on the order of 3-6ms.
 
You'll definitely want to look into the latency/dropout issue. As you can see from my signature. I run a MOTU 2408 with PCIe424 , and it can play pretty heavy projects (like the Cakewalk demos with all synths and FX unfrozen) with the buffer at 256, and all my usual stuff at 128. Have you run DPC Latency Checker or LatencyMon to check for spikes in Deferred Procedure Call times?
 
The real-time performance latency you're getting is due to a combination of MIDI transmission/response delay and audio latency. But you should be able to get the total down to about 10ms (playing the Fantom by echoed MIDI), which is quite tolerable, and soft synths will be better because they're only subject to inbound MIDI delay and outbound audio latency.
 
In addition to getting your buffer down, I think you need to do some simultaneous MIDI-Audio record tests from the Fantom - first with Local Control On, and then by echoed MIDI. And also maybe a MIDI and metronome loopback recordings to figure out where the delays and sync errors are. The more you understand about all the sources of delays in you system and the smaller you can make all of them, the better off you'll be. 
 
 
 
 
 
 
 

Update. On a hunch I removed all of my UAD-1 plugins and drivers. Now everything is much better, the response from my midi controller keyboard is virtually instantaneous and I was able to set my MOTU buffer down to 256 samples without any dropouts on a large project. I still have the 97ms midi - audio record delay but I can slide the tracks over to compensate. It's weird, the delay only happens when recording.

So if you record simultaneous audio and MIDI from the Fantom to a click with no Timing Offset in place, the MIDI timing is good but the audio lays down 97ms late? Or only if you record audio from existing MIDI playback?

Eureka! I found it, I had to tell Sonar to transmit MIDI Clock! Now when I play a MIDI drum track through the Fantom and record the audio with Sonar the leading edge of the kick is right on the measure marker. Much much better!
I can drop the MOTU down to 128 samples, but I do get random very short dropouts in large projects if I set the latency too low, have to experiment a bit more with those settings, but it's getting really close now. Thanks! :)