I already gave the solution to this problem above and also explained why it happens in the previous thread. It doesn't seem to happen to everyone. I'm one of the lucky few. In my case, my audio interface doesn't have MIDI so I use a separate MIDI/USB interface.

Manually correcting the alignment of every clip you record is not a solution; it's a workaround - and a pretty unpalatable one if you ask me. I'm sure that's essentially what the OP has been doing and is wanting to get way from.

Unpalatable, Brundlefly, really? Since this is an issue that doesn't happen to everyone, and it seems Cakewalk isn't going to address it any time soon, I see it as a solution. The OP has not been doing what I suggested, he and others have been guessing in order to get their tracks to line up. I found a way to make them line up perfectly without having to guess. The offset between the MIDI and the audio amounts to the round-trip latency reported to Sonar by the audio device. Once you enter that number in your Nudge settings, you don't have to deal with guessing. Highlight the clip or clips you just recorded and hit Nudge (which you can do with a single keystroke).

I recently investigated the MIDI timing issues when I bought a new and expensive MIDI interface; I had to realize that the MIDI performance in terms of latency and jitter is very dependent on the actual device handling the MIDI I/O but not on PC specs (I did get identical performance for different USB ports and 2 DAWs).
 
So I recommend first of all measuring the actual MIDI timing of your Fantom X (which is quick and easy; like I did here) and also give the Babyface MIDI ports a try. While many people claim that MIDI timing is not so great if MIDI I/O is just part of another device (and not a dedicated MIDI only device) I have found that among my MIDI devices the older Roland devices (audio interfaces) were the better, the newer (synth module used via USB) was not as good, and the expensive dedicated MIDI interface was the worst ... so eventually I got an ESI M4U XT for MIDI I/O which gave me best/most stable performance ... but as I said, give your options a check by measuring first to see if you could do better by just using another device or port ...

pinguinotuerto
The offset between the MIDI and the audio amounts to the round-trip latency reported to Sonar by the audio device.

Audio latency will not make your MIDI land early in the timeline, it will make it late, and it will be by the outbound audio latency only plus inbound MIDI transmission delay; this might happen to be close to audio RTL in a lot of cases, but that's just coincidence.
 
There will be a tendency for the performer to compensate for the combined audio and MIDI latency by playing early, but that's usually just a few milliseconds, and just makes up for the latency; there shouldn't be significant overcompensation. The exact result will depend on whether you're input monitoring or direct monitoring hardware synths driven by local control or echoed MIDI, or playing soft synths.
 
In any case, the OP and others have mentioned errors of 30 milliseconds or more (I recall seeing 75ms in one thread); that's much higher than any typical audio or MIDI transmission latency could account for, regardless of the direction. What you're doing may be working for you, but it's not going to be the right amount of nudge for everyone, and it should not be necessary with properly configured and working interfaces and drivers running at playable latencies.

Dupe Post.

pinguinotuerto
Unpalatable, Brundlefly, really? Since this is an issue that doesn't happen to everyone, and it seems Cakewalk isn't going to address it any time soon, I see it as a solution. 

No, it's a workaround as it doesn't address the root cause.