Hi Wyn, this paper looks at PLL jitter which indeed is a well-established source for distortion.
Maty, however, seems to experience audible differences based on compressed versus uncompressed FLAC.
The contention lies in the fact that FLAC decodes to 100% bit-perfect PCM, and that a USB
interface between PC and DAC cannot be the source of jitter when it operates as a pure a-synchronous data interface. Once the data is safely & timely out of the PC there is no way for the DAC to be influenced by the FLAC encoding unless the USB data stream can be corrupted without detection (or if the USB data buffer depletes).
Writing the above I suddenly realized we didn't ask
@maty how exactly his DAC is connected to the PC.
Do you use USB or are you using optical or electrical SPDIF? If you're using SPDIF you may well experience all kinds of unexpected distortion: there is no error-correction in the bit stream and PC clock itself may be a jitter source. Even the circuit generating the optical signal may be subject to noise and even timing fluctuations.
Link: a simple experiment by Serene/Audio showing how an external USB converter can actually make things worse!