Sounds like everything is okay if the amp is displaying Dolby TrueHD, but to clear it all up, it depends what soundtrack is used on the disc. Basically, on DVD, there were really only a few formats used ranging from Dolby Digital 2.0 to 5.1 and DTS. These are compression formats which allow the studios to compress the soundtrack of the movie to fit on the DVD. So in the case of the Dolby PLiix on the amp - this means the DVD is using Dolby Pro Logic standard and the amp is receiving this and decoding it.
On Blu-Rays, because of the extra space available, a whole load of new encoding formats were designed including Dolby TrueHD and DTS HD Master Audio. These are basically new standards which still compress the soundtrack, but do it losslessly, meaning you get a much better quality soundtrack on the disc than the old formats (much like an Apple Lossless or FLAC version of a song (or any other lossless compression you care to mention) sounds much better than an MP3 of that song which is compressed down to 128 Kbps for example).
So have a look at the back of the box of your Blu-Rays and see which soundtrack is included. If you have Dolby TrueHD or DTS HD Master Audio, or better still uncompressed PCM (i.e. no compression is used at all), make sure you select this soundtrack on the disc. The Yamaha should then tell you what it's receiving and you know you're getting the best sound possible.