The sound of pennies dropping . . . everywhere experimenters are discovering that one bit-perfect computer can sound very different to another bit-perfect computer. Fortunately that dinosaur of an IT adage - 'bits are bit' - is en-route to extinction!
It's not voodoo: it's about bitstream timing errors and resultant jitter, and the problems created by cheap, noisy - highly compacted - components on the PC motherboard and its cheap noisy power supply.
Here's a handy guide to what jitter is, and sounds like:
http://www.antelopeaudio.com/en/digital_clocking.html
Macs call for a two-pronged approach: do everything possible to suppress hardware gremlins (remove or turn off bluetooth/wireless, swap HD for SSD, change the power supply, isolate / clean the 5V USB rail, etc). Then, as doug2507 sagely points out, look hard at the software: shutting down redundant processes and streaming file to RAM using Pure Music, Decibel or Audirvana all bring rewards.
As Keith is always keen to point out, async USB and Firewire are easier for computers to handle than SPDIF or balanced digital. But a USB cable is inevitably the data cable filling in a power cable sandwich, so you have to deal somewhere with the electrical problems created by powering chipsets in the DAC with your noisy computer.
On the other hand, giving a DAC SPDIF or AES/EBU involves taking charge of the clocking, which is a tough process to get right. Almost invariably, when a DAC has a balanced input, it sounds better this way - so tackling USB > AES/EBU conversion is often well worth the trouble. Wyred 4 Sound, for instance, recommends USB above the DAC2's SPDIF, optical or balanced digital inputs, and yet without a specialised audio computer, I think it's conspicuously better via AES/EBU. YMMV.
D-A stages have come a long way since the heyday of the high-end CD player, but as SPDIF transports, a computer is ironically far less sophisticated, for all its processing power (none of it 'designed for audio'). Directly comparing digital output from a good CD player with a computer is often enlightening - and dispiriting for fans of computer audio. Then again, we can do 24/192 . . . try that on your Naim CD5.