AudioSnap issue - Need help from the gurus...

AudioSnap is one feature I have not used in Sonar so consider this a noob question...
 
I want to create a cover of an existing song (including tempo variations) which I imported into Sonar. I enabled AudioSnap on the existing song track, and then in the AudioSnap palette selected Tempo > Set Project from Clip. This created a tempo map for the whole project that matches quite well with the song, which has a somewhat varying tempo throughout, with average tempo of 171 (the song is Surrender by ELO if you want to try and repro the issue).
 
However, there are 3 measures where the tempo map have not been set properly. The weird thing is that the transient markers around these measures are exactly on the correct places in the clip, however for some reason Sonar misaligned the song measures with these transient markers (everywhere else the markers are spot-on with the measure start positions).
 
To explain better, see this:
 
Image link [can't get embedded link to work, sorry]
 
Notice how the markers up to measure 18 are aligned properly with the measures. However measures 19, 20 and 21 are lagging the markers, meaning the tempo for measure 18 was set too slow, resulting in measure 19 starting late. However at measure 22, things are back in sync again, and is so for the rest of the song.
 
I played with all the AudioSnap settings, however it insists on starting those measures late no matter what I set the options to. To confirm again, the markers at measures 19, 20 and 21 are at the correct transient positions in the song, so moving them will not fix the problem since they are already at the correct locations.
 
I also know I can edit the tempo map manually but I'd like to rely on AudioSnap to do it since editing it will make everything later in the song be incorrect timing wise.
 
So do any of the AudioSnap gurus know how to get it to sync everything up properly?

Beepster
I may be misunderstanding the issue but the simplest way to correct those off beat/measures is to right click on the timeline and select "Insert Beat/Measure" (I think that's the menu option but it has been a while) where the beat or measure should be and a dialog will pop up that gives you options for adjusting such things.
 
Sorry... awkward explanation because as I said it has been a while but you'll see what I mean if you can find the option. Cheers.

If I understand correctly, you mean I should put the Now time exactly on the marker (the one closest to measure 19), and then right-click on the timeline and select "Set Measure/Beat at Now". Then select the start of measure 19.
 
If I do that, what happens is that Sonar inserts a large tempo spike (350) between those 2 points to try and let it catch up, which is not the correct result. The correct result would be to adjust the tempo across all of measure 18 so that the next marker starts exactly on measure 19.
 
What I also tried:

• Right-click on the marker that falls just before measure 19, and choose "Stretch to..." and then select 19:01. However as expected this stretches the whole of measure 18 to fit it to its too-slow tempo. The audio itself should not be stretched so this is the incorrect behavior.
• Right-click on the marker that falls just before measure 19, and choose "Move to..." and then select 19:01. This time the marker itself is moved to align with the start of measure 19, meaning the marker is now no longer at the correctly detected transient. So this is also not the correct behavior.

Any more ideas?

Beepster, no there are no missed/skipped/extra beats during the problematic measures (see screenshot).
 
One thing I did notice while looking at the tempo map... Some of the tempo changes don't happen exactly on the start of the measure. I would have thought AudioSnap would assume that those detected transients are on measure boundaries (they are actually detected 100% correctly on the measure boundaries which is why this is confusing to me). So this is probably part of the problem.
 
I would have thought that when AudioSnap resolution is set to "Whole" that it would only consider transients to be on measure boundaries.

BTW... I do most of this stuff manually because I find the auto detect pretty useless for the wild fluctuations in some of the tracks I've tried it on. Cheers.