We just received a bunch of notices a month or so ago about the 2.6% for orders from last year and now fedex is billing them to our shipping account.

After the first charge of $2000 was approved by the CC we got that cc to stop accepting charges from Fedex, so nothing else would be automatically paid. 

Now it's up to $13k owed.

Any advice on dealing with this?  Does fedex typically accept a small settlement amount after awhile if the bills remain unpaid? 

We never signed any agreement with fedex allowing them to bill these customs charges to our shipping account, or any agreement with them allowing them to put negative marks on our credit if these customs bills went unpaid - but since they are now stuck under our shipping account incorrectly, they presumably could.