I noticed the tracked music as well. Particularly when they're trying to land Greivous' ship with that rehashed "Anakin blowing up the droid control ship" music from TPM and the teaser trailer. I agree that the "happy march" when Obi-Wan linked up with Bail Organa's cruiser was inappropriately upbeat when juxtaposed with the events in the previous scene. Like you, I noticed it.

I was also annoyed that 50% of the music in the film was NOT included on the CD soundtrack. Which means, they need to release an Ultimate Edition (they didn't for AOTC) real soon.

But, this is just nitpicky stuff. Overall, I was very satisfied with the film and enjoyed it immensely.