Wow, when you posted this I knew exactly what you meant. I have a Viking Sapphire 875Q - I've had it for 1 1/2 yrs. About a month ago - I was sewing along and stopped to move some thread out of the way - well the pressure foot came down on my finger and barely was poked by the needle - after that my machine started clunking - I redid everything - rethread, change needle etc. Took it in to be repaired - thought it was just simple - no they told me the same thing - then they tried to make me pay for the repairs - I refused because its still under warranty - they called me back and apologized then they repaired it and I did not have to pay - the part was over $ 300.00 - I kept saying to them - why would my machine go bad over my finger - it wasn't like I jammed it in there or abused it - accidents happen and the machine should be built to withstand those kinds of accidents. They said the feed dog mechanism was damaged and the shaft was flexing ???? It sounds like you have the same problem.
In the end, it turned out well, they repaired it and now it runs great again - but it was a tense two weeks while I waited. Just remind them of your warranty and I hope this all works out for you - you can pm me if you need more info. Good luck.