I have had the same problem with my PS3 and my Marantz SR8001. I noticed the crackle a while ago, and so far have experienced it in about every movie with TrueHD audio on Blu-ray. I initially thought it was my center speaker, so I swapped that out with no improvement. I then swapped cables, and still no luck. I tested all possible audio outputs on the PS3 and all matrix methods on my receiver. I went as far as putting my Marantz MM-9000 for my amp and bypassing the SR8001's internal amp. Same crackle sound. I tried on my friend's PS3 in my stereo and still it crackled.
That pretty much leaves only the processor and source. However, my receiver plays music beautifully and I never noticed a problem on DTS-MA discs.
J Garcia: Check the beginning of track 14 on Iron Man and tell me if you notice the crackle.
After a lot of research, it seems it might be the source itself. However, quite a few posts online are popping up with this issue, so it is possible that Sony has messed something up with one of their newer firmware upgrades.
In summary: no one freakin' knows and more and more people are getting annoyed by it