Usually the best way to be sure that the message is from eBay is to check your messages within eBay.

If it is genuine you will have a duplicate of the email in your messages section. You can then be sure that it has come from them, and just comply with their request. 

If you do nothing you will continue to have issues and eventually a harder problem to solve.

Many sellers have had hiccups with the change over to the new MP system, try to work though them and eventually the sales and $'s do begin to flow. 

Good Luck