I believe there still are some idiosyncrasies in the way Sonar 3 handles meter changes that take some getting used to. I'm just finishing a piece for chorus and soundscape that's about 150 measures long with various meters throughout, 9/4, 6/4, 3/2, 4/2, 2/2, etc. I think you can duplicate the problem I encounter Ron, if you adjust your test sequence to have more than 2 measures of each meter and do the following:
For instance, if m.1 - 7/4, m.7 - 4/4, m.12 - 7/4, m.18 - 4/4.
Now, if you change the meter for m.9 to 5/4, I believe you'll see that m.9-11 will all change to 5/4 and skew the notation 1 beat from m.10 on, which may be understandable, but not necessarily what you would expect or want to happen.
If I've written 6 measures of 4/4 music from m.7-12, and decide one chord needs to be extended 1 beat and make the meter for that measure 5/4, I don't want the following measures up to the next meter signature to change, as well.
Work arounds are to re-enter the correct meter for the measure after your change (m.10 back to 4/4/, in this example), or at the onset, enter the meter signature for every measure in the sequence, which is time consuming at the beginning, but worthwhile later on. I do believe, even after correcting the meter issue using either work around, you'll need to go back and adjust all the clips (in other tracks) that were affected by the meter change.
What I was expecting Sonar to do was behave as notation programs such as Finale. That is, if I change the meter in one measure, all other measures would be unaffected, unless I specify the change to be over a range of measures.
This is not that problematic for me. I write my choral scores in Finale and create the soundscape sequences in Sonar. However, I do import a midi file of my choral score and insert it into the soundscape for reference, and this is where I noticed the problem. As I created the soundscape, and changed meters preceding the choral clip, the choral clip would become skewed by the amount of change.