Hi fboe,
When you are using the I2S output from the hifiberry digi+ pro I assume you also supply a master clock signal (connections GND, DATA, LRCK, BCK & MCLK). The src4392 then works in slave mode.
When attached directly to the pi there is no master clock signal available and the src4392 works (automatically) in master mode. The src4392 then generates its own master clock signal at a frequency derived from the available signals (connections GND, DATA, LRCK & BCK).
It is possible that the src4392 loses track of the word length when paused in master mode, this would cause noise or clicks. The default word length for the src4392 is 24bits. But the Hifiberry Dac driver works in 16bit or 24bit mode. A possible solution could be to force the Hifiberry Dac driver to always use 24bit mode.
Instructions for the fix and an explanation (for a totally different problem) are here
#41671
Janui