It would appear that a typical soundcard isn't stable enough for VLF use when stations are running 1mHz bandwidth signalling, and using any locking option to other off-air signals is a bit restrictive in what software you can run.

 

It may be worth looking at a custom codec driven from a locked frequency source.   The PCM2900 (which costs only a few pounds from Farnell, and they supply the data sheet) is a self contained USB codec which needs only a handful of additional components for a USB soundcard with stereo line input and output.     For normal operation it needs a 12MHz crystal, but an external 12MHz source can be used which could be locked to, or derived from, a high stability reference.  Even a TCXO on its own with typically 1ppm accuracy / stability would be better than any normal 20ppm crystal

 

I've built one of these codecs, but have yet to confirm the resulting sampling rate(s) are exactly what they should be.  By the time it has gone through USB packetising and Windows'  drivers I hope full synchronicity is maintained right through to the user software.   This may only be the case for sampling rates like 12000Hz - it all depends what windows does.   Exact conversion is needed for this solution to be worthwhile, not just a close approximation.

 

Andy