I tried with air strike 2.

strike 2 + waves aphex -> No problem.
Strike 2 + Alloy 2 with multiband option -> Problematic.
Strike 2 + Ally 2 without multiband option -> No problem.

All of a sudden after an update (three times in a row) things happen.

Wav file + alloy2 with multiband option -> problematic.

Now I think I can confirm that Alloy has a issue, and AD2 has a issue.

I guess it is Sonar's end. Maybe i'm wrong... Maybe not.....

In the link scook referenced, this comment may be helpful:
 
The phase error seems always to be exactly 64 samples, so in lieu of adding some other audio track sending to the parallel bus, the phase error can be compensated by adding a 64-sample delay to the parallel bus using Channel Tools or some other sample-delay plugin.

Anderton
In the link scook referenced, this comment may be helpful:
 
The phase error seems always to be exactly 64 samples, so in lieu of adding some other audio track sending to the parallel bus, the phase error can be compensated by adding a 64-sample delay to the parallel bus using Channel Tools or some other sample-delay plugin.

Even if this may provide a workaround (it seems to work in the project where I had encountered the problem) that would still be unacceptable in terms of usability - who can guarantee it will be the same number in the next troublesome plugin combination?
 
It's not that easy to determine the correct offset in #samples if it happens on a bus (waveform preview is only "sketchy" i.e. it's not possible to jump to transients and determine samples between transient peaks.)
 
Sonar needs to handle this properly. It's part of proper PDC. If we can "fix" this by adding 64 samples delay, Sonar programmers will be able to find a solution which does it automatically.
 

64 sample trick works for me in AD2 Case.
But for alloy, it does not work, and i can not find proper sample number for trick.

Looks like normal track is 7~8 samples faster than alloy-ed track. I'm not sure.

Would the latency for Alloy vary because it's a multieffects? Does it have lookahead?

Alloy has zero latency menu, no help.
And i use only multiband comp in this case!

Hmmm...I think a multiband comp might have a lookahead. I don't know.