The lead I use it a typical 2:1 with line plugs since thats where I'm taking the output from on my mixer.

Oh one other thing that just popped into my head as I used to have a similair problem as this, was that my pc was just too slow to record all the sound which would always lead to artifacting the sound. If you've just upgraded though I could be barking up the wrong tree but have you reinstaleld the latest sound drivers for your new card? Using incorrect ones could bugger it up for you.

What sort of spec is your PC?