Acrobat is using lossy JPEG compression (quality: medium) on some images after transparent objects were flattened. Even if the images had a ZIP compression before, Acrobat will use a lossy JPEG compression. The result is a loss of quality. There are also differences in quality within a single image, cause some images are divided in parts with a ZIP compression and with a lossy JPEG compression.
Is there a workaround to use Acrobat's transparency flattening without JPEG compression? The problem appears in Acrobat 7, 8 and 9.