Hi gattausen. I'm not sure I can help, but I'll try. There could be a few different things going on. I just want to point out a couple of things first. Please make sure that your receiver is set to the auto detect mode, that way it can decide what decoding format fits best and turn on the appropriate speakers. Secondly (I'm not saying this to be mean or talk down to you, I'm just making sure you know) you have to run either an optical cable or a digital coax cable from your DVD player to your receiver. You did not complain about problems with Dolby Digital, so I assume that you are already doing this, but if you're not then you'll have to get one or the other. On to the help, or my best try to do so anyway:
First off you can turn up the volume to those rear speakers directly. Refer to PG. 46 of your manual for how to do that. If only the L & R lights on the display are enabled during Prologic and prologicII then there may not be a problem at all. Many budget receivers will only show those two speakers lit up in every mode except digital ones. I don't think this is actually a problem at all. Another thing to make note of is that lot of older movies that don't have Dolby digital soundtracks aren't going to sound loud out of the rear speakers. The recording quality simply won't allow this. Although I've heard some really nice things about prologicIIx.
Lastly as to the problem with the sound on DTS I'm pretty sure I know whats going on. It most likely has nothing to do with your receiver but instead stems from the settings within your DVD player. You have to go into the set up menu of your DVD player and enable it to play DTS. Many DVD players come from the factory without this setting turned on for some reason. On my dvd player I have to go into my main setup menu, select audio from the drop down menu, select DTS, and make sure it is enabled. It should be pretty similar for you, and once you do so all the speaker lights should come on.
I hope my answers help, but if they don't please post back. Also it would be nice if a yamaha user posted as to whether or not their display shows all speakers in pl and plII modes. Good luck with getting it all going smooth.