I think Noel or someone had explained a bit about that timing offset. It is, if I recall, what you would need to use if the auto-calculated compensation isn't doing it for you.
I haven't yet found his post, but here is something from another thread talking about fixing that issue:
brundlefly
For those who just have to have everything as perfect as can be, they can do this analog loopback recording, zoom the waveforms, nudge the recording back one sample at a time until it aligns perfectly with the original, and add this number of samples as a manual offset.
Actually, just Zoom in real far until you can see each sample (obviously you want to set the Time Ruler to show samples) and then count the offset between the two waveforms. Enter that value in the offset box and you're done :-) Sonar is great though, and like Brundle said, this is really not a big issue anymore. Keep up the good work Cakewalk!
And from the Sonar doc:
Record Latency Adjustment (samples)
If you loop an audio output back into an audio input, and re-record a track this way, the audio doesn’t line up. For some sound cards, it is off quite significantly. This record latency adjustment is a compensation for that delay.
You can do an approximate measurement of the delay by turning on samples as the resolution unit in the Time Ruler, and comparing the original track with the re-recorded track. Then you can enter a value in the Manual Offset field to compensate.
If you use ASIO mode, enter 0 in the Manual Offset field and leave the Reported Input Latency check box checked (this check box only appears in ASIO mode). This will line up audio in most cases. If you think you can tweak it closer, use the Manual Offset field.
In ASIO mode, the current active ASIO device (remember ASIO can only have one active at a time) reports its “Input Latency.” You can't edit this value. This supposedly accounts for buffer size, A/D Conversion latency, etc. The check box allows you to use this reported value. It is checked by default. In any case, the amount entered into the Manual Offsetfield will be combined (added to) the reported value if you have it checked.
And lastly from the web:
Count the distance in samples by putting the Sonar time ruler in sample measurements instead of h:mm or bars and zoom way in so you can see the individual sample steps. Locate the beginning of each ping and make a note of hte sample address for each. Subtract the sample address of the original reference ping from the new overdub's sample address. If the overdubs are behind, the difference should be a positive number. That's the value that overdubs are misaligned behind pre-existing tracks.
I hope some of that helps,
Bob Bone