Adam I'm surprised by the results.
I've used CS3 in the past and now CS4 for quite a lot of stitches with very few issues. This includes one with 15 shots. What really confuses me is the perfectly straight lines you're seeing - this is not at all typical of the way CS4 stitches.
I do them all directly from CS4 and not via LR, but that shouldn't be an issue.
Workflow is:
File > Automate > Photomerge
Choose "auto" and tick "Blend Images Together". Vignette removal and Geometric Distortion Correction are optional.
The typical stitch when viewed in layers shows stitch lines that are anything but straight.
I do at times have issues and some manual adjustment helps. Here's just one recent example that of a 5 shot stitch in portrait orientation (A700, tripod, Manfrotto pano head and levelling plate, 50mm f/1.4 lens, cable release, MLU, 30 second exposures in case any of it is important) - done from DNGs.

Merits of the image or otherwise aside, I don't see any stitching issues.
Having said all this, a colleague and I have been using PTGui beta and decided to purchase it for an improved workflow and results so I have to agree with others that PTGui is an excellent choice and offers many more features. However, CS4 shouldn't be giving the results you're seeing.
Can you post your exact workflow?