I may have an answer for you. I usually record @ 44.1khz 16bit at 320kbps mp3 on MC5, but i've been asked to re-produce some of my songs @ 48Khz 24bit as a .wav file. I was hearing crackles just like you describe when i've re-encoded the song using MC5.
If you want to find out what is causing the artifacts read on, or skip to the last paragraph for my fix, Solo each stem and encode it in 24bit as a .wav , and once you're done. Open a new MC project and load all the 24bit wav stems in and solo each one until you find the crackle / artifact etc.. is coming from. Then at least you know whats wrong. For me it was a VSti add-on a String Double Bass from Garritan Big Band 3 that was causing all the crackling as it wasn't being rendered properly by MC5. (sounded great within MC5 playing it, but after encoding / rendering it down to 24bit the crackling appeared)
Anyway to cut to the chase, i fiddled around with settings, and the one that worked for me was to 'untick' the box that says 'Use High Priority Threads For The Audio Engine' . Which is in <File> <Preferences> <Sound Device> . Wasted a whole day out of my life finding the fix that worked for me, hope it works for you mate. Cheers Mark