Your other employees might not have been caught by the match yet, if this was a global problem on your account. Or it may just be a database error by the IRS (they lost it).
Did you file your W-2s and W-3 electronically or on paper?
I would start by checking your submission and make sure that this employee's name, address and SSN are correct on your copy of the filed information.
I really don't know whether you should send an entire new filing, or just send a W-2C to the IRS and the employee (that way you get it in the system without it being a duplicate), or just send an original W-2. You don't want the IRS to suddenly go from thinking there is no W-2 to thinking there are two with twice as much income.
You might want to ask an enrolled agent for advice, or try calling the IRS yourself.
My gut feeling is to send this employee and the IRS a W-2C.
Meanwhile, the employee should be able to send the bank a copy of the W-2 even if the IRS transcript doesn't match it. The bank may also accept a certified letter from you as income verification.
