I would google the specifics of your amp model for an answer or ask somewhere like AVForums, you have told MP/windows to output only stereo sound so thats all your amp is giving you, you need to tell the amp to split some of that sound to the sub, dolby pro logic etc doesn't add a sub channel as far as i remember, just adds pseudo centre and left and right channels at the rear. so even with pro logic/logic 2 enabled on the amp you still wont get a sub channel.
It could be that your amp cannot do this, I know the Onkyo's can, which you had (and it worked), Id imagine a yamaha could though as they are good amps unless you have a very budget model that doesn't have the feature.
Sorry, I'm such an idiot. I had it set to small speakers on the Windows config but it was set to large speakers on the amp settings. Changed this to small for all speakers and now I have bass from my sub
Thanks for all who contributed as you pointed me in the right direction.