All DACs that support both 44.1 and 48 Khz sampling rates and their multiplies have two clocks- one for each base frequency. Every time the DAC swithces between these two clocks, you will hear a relay-like clicking sound coming from within.
Also, if there is a longer pause between tracks, the DAC might unlock from the signal and then lock onto it a second later at which point you will also hear this click.
Not all DACs behave this way but generally, in both cases, this is perfectly normal.
That being said, this 'click' sound isn't produced by the actual clock generator but by the input receiver chip. I would need to know the exact chip used in your DAC to know for certain, but this chip is resposnible for input selection as well as translating data to the DAC chip and, if there is one, the sampling-rate converter chip.
BDA-1, 2 and 3 input recivers already incorporate an SRC so there is no need for a separate chip. I believe they use an SRC4392 by TI. Your built-in DAC might be using a CS8416 by Cirrus Logic which is also good but perhaps a little less imuune to input jitter. For me, that wouldn't be enough of a reason to spend money on a new DAC.
Cheers,
Antun