It does sound something like there's digital clipping just on the transient peaks.

I'm not saying that's definitely what it is, but without looking at the original uncompressed wave-form greatly magnified to see what the transient peaks look like, that's one thing I'd suspect. Inter-sample clipping maybe?

Is the audio source a pre-recorded commercial track, played by software synths/sampler or recorded via the interface? I've come across something similar sounding caused by poor or corroded cable to plug connections in audio leads

The offending clicks can be seen clearly when zooming in on the waveform.  The nice sinusoidal audio waveform has several samples of glitches/corruption around the clicks.  The glitches occur simultaneously on both channels.  Doesn't appear to be clipping.   It looks like some bits are getting lost in the sample.
 
Just checking on your setup ... I'm assuming the recorded audio is via an analog input on the MOTU (i.e. not, bounced soft synth samples).  Given that assumption, many of the above suggestions seem like a good place to start.   But, looks like you've tried some of those already. 
 
Another thing to check is the MOTU clock source. Perhaps that changed somehow. For my RME, this setting is located under the SONAR  Preferences>Audio Driver Settings and pressing the "ASIO Panel" button.  If there's not external HW clocking, the clock source should usually be set to "Internal".
 
Maybe my first paragraph will help someone recognize the problem.   As you say, it might be the MOTU unit. 
 
P.S.  'jpeterson' posted similar info about the audio waveform glitches a few minutes before my post.

tlw
It does sound something like there's digital clipping just on the transient peaks.

I'm not saying that's definitely what it is, but without looking at the original uncompressed wave-form greatly magnified to see what the transient peaks look like, that's one thing I'd suspect. Inter-sample clipping maybe?

Is the audio source a pre-recorded commercial track, played by software synths/sampler or recorded via the interface? I've come across something similar sounding caused by poor or corroded cable to plug connections in audio leads

I've tried two audio sources, from a 2nd computer that is dedicated to my VSL library, the midi tracks go into it via ethernet and come out via ADAT into the MOTU 1248.   I also used a soft synth in my DAW as an audio source, same problem.  I can rule out the VSL machine and ADAT because when I take it out of the equation, the problem still remains.  It must be Sonar or the 1248.  My levels are very moderate, not even near clipping levels.  I monitor every source and every destination, can find no clipping throughout the signal path.   MIDI playback is flawless, it's only when I record and playback the wave file that the crackling occurs. 
 
 
 

I had a similar sound earlier this year.  I cleaned up my studio and in the process I moved my router.  It was to close to my computer and that was causing the problems.  When I moved it back a few inches the problems went away.  YMMV.

Is it perhaps a bad or loose cable inside the computer? I'm thinking the SATA cables that run from the MB controller to the drive. It doesn't sound like clipping to me. More like static. If you can play midi stuff and it sounds good, then you've sort of cleared the interface and Sonar. If you can do direct monitoring and it sounds ok but you hear ticks from the version that printed to disk, then it would point more to an issue inside the box.
 
ANy recent windows updates that may have turned on the wi-fi or onboard audio etc. without you knowing?

MIDI works. Then the interface must be fine, too.
What if you play back a WAV or MP3 using just Windows Media Player (anything but Sonar)?
...I mean, of course, a WAV or MP3 that is proven to be OK - not one you record now!

jpetersen
MIDI works. Then the interface must be fine, too.
What if you play back a WAV or MP3 using just Windows Media Player (anything but Sonar)?

playback of midi files and wave files already created before today playback fine.  It's only when I try to record.
 

ampfixer
Is it perhaps a bad or loose cable inside the computer? I'm thinking the SATA cables that run from the MB controller to the drive. It doesn't sound like clipping to me. More like static. If you can play midi stuff and it sounds good, then you've sort of cleared the interface and Sonar. If you can do direct monitoring and it sounds ok but you hear ticks from the version that printed to disk, then it would point more to an issue inside the box.
 
ANy recent windows updates that may have turned on the wi-fi or onboard audio etc. without you knowing?

Yeah, that what it sounds like to me static, rather than clipping.  I don't think any changes to Windows or wifi but I'll check again...

thanks everybody for trying to help, very much appreciated...
 

OK. Then it can still be the interface.
Is this the only interface you have? (I have 8!)
Trying to determine if its Sonar or the interface.