although its not needed, but since you are getting a much bigger bass output in the prologic mode is why you could continue using the PL mode. prologic decoding is neither discrete nor precise. it usually fills the audio track with continuous/consistent low frequency (even in scenes where it shouldn't have been prominent, like people talking, birds flying, etc.), whereas in the normal mode (ie, am talking about digital decoding), the sound output is discrete and precise, and bass is prominent only where its meant to be (big dramatic background sound effect, explosions, etc.). although i rarely watch movies on my HT speakers connected to my PC, but on the ones that are connected to my TV and media player, i've found that they reproduce a far better output in every way, if the source is having a DD 5.1 or DTS-HD kind of sound-encoding, than a simple stereo encode, although i can only use 2RCA (stereo) as input to the HT (this is truer when a DVD is used as a source). this may be perhaps because dolby digital more-or-less retains its sharpness after decode. though this shouldn't concern you, as you are using your speakers with your PC. now am not sure, but what may be happening in your speaker's 'normal' mode is that your onboard audio-processor might be decoding the digitally encoded audio-source (the pro logic decoder of the HT being bypassed), and the sound is then fed to the various channels (these can't be directly fed as they are discrete digital sound-channels, and will have to decoded for analog use). hence in this case, the bass output may be close to how it was meant to be actually, and not synthesised like how pro logic does it.
check the review of f6000 from the link that i had posted earlier in this thread. i re-read it, and found the reviewer telling that in the surround sound mode (which could be the 'normal' mode), he found the bass to be feeble. may be its a defect/property inherent to this system, or perhaps requires some tweaking. do one thing. if you can, get a DVD of the movie 'master and commander' (much recommended), else, a blu ray disc, or even if not that, then may be a *ahem*. this movie has terrific surround effects, but only at the right places, in the right amounts. play this in a software like powerdvd, and check how's the bass response in the first skirmish that takes place after the movie begins (cannon-sounds and explosion-effects and all). also, in the meanwhile, do post a few screens of what settings you are using in your realtek sound manager software, and your video player of choice. may help. and yes, does the manual mention anything about pro logic, whether is pro logic I or II? should be II, as I has become almost obsolete now, and II's better.
and nothing stupid in it. its quite confusing and complicated, and people who seem to know their way in this territory also usually don't agree on one topic or the other. and we are only sitting and speculating on this from atop a fence on its border.