Due to the smaller percentage of the disc required to use uncompressed audio for either hi-def format, as well as the availability of Dolby TrueHD as a mandatory audio format for HD DVD, it's fairly common for releases in both formats to include lossless audio.
Paramount's delay in using lossless audio on their discs likely stems from releasing discs in both formats. HD DVD's smaller storage capacity and inclusion of the compressed Dolby TrueHD as a mandatory audio format make that the obvious choice. However, since it's not a mandatory format for Blu-ray, another audio stream must be included on those discs if TrueHD is to be included.
Fortunately Blu-ray's increased size makes that posibble. However, that doesn't mean it makes sense to use different versions for each format. However, that appears to be exactly how the studio will be handling the issue.
This is an interesting result of the format war. As a supporter of both formats Paramount has no pressure on them to take advantage of either format's strongest features. Instead it makes more sense to look at the company's bottom line and use the same audio for each.
If not for complaints from consumers this move may never have happened.
Source: High-Def Digest