It sounds like you did everything correctly...but something this sort of thing happens.
My suggestion is this: Since you have to reply to the IRS letter, go ahead and reply with an attached completed form 843 and say the following:
1. Full names and EINs of the companies, as well as a brief history of how two companies ended up with the same EIN.
2. Include a statement that your employer refuses to refund the excess to you; therefore, having to repay the IRS while being unable to collect from the company would be a hardship on you. Quoting or even photocopying the reply would be helpful, along with the name and title of the person that told you this (oh, and his/her contact info). Give the IRS agent the chance to pick up the phone or dash off a form letter to the company telling the company to pay up.
3. Ask the IRS agent if he/she would accept this 843 in lieu of the repayment of the excess, since the point of the 843 is to get the excess refunded to you anyway.
The agent may say "OK", or may reply that you have to pay the excess pay and await the refund as the 843 is processed. But since you will have answered within the required time frame for the first letter, you shouldn't be penalized, and it may give the agent an opportunity to ask you for more information (or, of course, to just to tell you to mail it to wherever).
Nothing ventures, nothing gained.
