This has plagued me for years. Anytime the PSM or Brisque rips a file that contains CT images on top of each other, the resulting CT has jaggy, non-anti-aliased (or just aliased, I guess) edges where the 2 images meet.
Here's an example. I created this logo as part of a brochure in InDesign. Because I'm using ID's drop shadows, I want to force the white type into the CT so I don't get any "jumps" in the lines where a LW item becomes CT to accomodate the shadow, so I force it to CT by placing a white (blank) .PSD over the entire logo and set it to multiply. In the image below, the top one is Brisque's ripped CT of this, and the type edges are jaggy. In the lower example, the entire thing is assembled in Photoshop and the edges are nice and pretty. Before anyone tries to blame InDesign, this can also occur in Quark files where you might have a background image with clipping path images floating on top.
Sometimes, it is helped by setting the CT edges to use LW resolution, but often times this takes forever to rip and doesn't always rip correctly. It can also be improved by upping the CT res in Preferences, but then I am needlessly upsampling the rest of the file. I've also tried setting the Brisque or PSM Prefs to use Bicubic interpolation when generating the CT, but this does not change the results.
Anyone noticed this issue, and have you developed any other workarounds?