1: we should probably not be discussing pirated stuff. I'm not talking about morality here. It's a liability issue for us, the users, and the site. Remember that all of our posts are captured by places like internet archives and search engines/other spidering software. Once it's on the internet, it won't ever completely disappear.
Anyway, on to your concerns: I've experienced this crackling with lossless files that I made from CDs I purchased (for the record, if the idiotic RIAA is snooping around- pun intended) . I think this is for a couple reasons: A mismatch between the sampling speeds of stuff in the processing chain seems to make it worse.
We have 44.1kHz from the CD. The data goes CD>FLAC encoder>FLAC Player>OS Audio Framework>Hardware Driver>other-non-important-for-this-argument-goodies>DAC USB to S/PDIF converter>S/PDIF to I2C converter>DAC chip. If at any time there is a mismatch with sampling frequencies (say, to the popular 48kHz that is mandatory in some sound codecs), or larger than normal mismatches between your computer and the DAC's hardware clocks (happens occasionally), there is the possibility of small gaps or artefacts if the resampling is done poorly. Usually, though, mismatches are so small that you won't notice them. That's in part why some really high end stuff has external, shared clocks, and why some of us have to buy HiFace reclockers if we have wonky computers.
Analogy: Cinemas use 24FPS. American NTSC broadcast standards are at 30FPS. They shortcut often by periodically repeating the same frame, which is why you see scrolling credits stutter and jerk around. Also similar issues in Video Gaming are called "screen tearing," and that's why us gamers have vertical sync and fancy frame buffering software.
Hopefully, anyway, all the steps in the audio path can interpolate well, if they insist on doing so, but sometimes it doesn't work out.
Also: If your CPU is taxed, your USB/PCI lanes are saturated, you are low on RAM, or you have long hard disk queues, audio buffers can run out as they are shockingly small. Increasing buffers can help, if you can (rare), at the cost of increased latency. My HiFace+Amarra doesn't crackle at all, but it has a ridiculous 2.4 second delay. Highly irritating.
Also, slightly damaged files (I'm not sure if FLAC has comprehensive ECC, but I highly doubt it) can result in small parts failing OS checksums, resulting in crackling (also known as millisecond long cutouts) as the FLAC codecs attempt to skip over damaged sections (like skipping CDs).