I have had similar issues. Last year my employer somehow didn't transmit my w2 to the IRS. So they had no record of my earnings or tax withholding. So I was mailed a notice, CP 05. Which can be reviewed up to 60 days. I sent in my own w2 copy by mail but it didn't take long at all once I did that.
Well imagine my surprise when AGAIN this year the same crap happened. No w2 submitted by the SAME EMPLOYER. When I called the IRS last Friday, she told me I was being mailed a notice (again CP 05). She said they had not received any w2 on my ss#. So they have to verify my wages & tax withholding. I asked her for the address to submit it to, just to get a jump on it (as I have not received the letter yet). I did this same thing last year and it sped up the process.
What I suggest is, if you have not received a letter and are still waiting on your refund, call the 1040 number for the IRS. Not the 1924 number. They CAN tell you what notice is being sent and what it pertains to and what they are requesting from you. They can give you the address or fax number in which you need to submit the requested info. Get a jump on it. Don't wait for the notice. That will speed up the process.
I'm not sure why so many have been chosen for review this year.... maybe a huge increase in fraud. But I also know that back in the day, employers didn't have to transmit our w2s for us to receive our refunds. Now they do. So there is alot of room for error on the employer's part when they're submitting the w2s. Take it from someone that has been reviewed the last 4 outta 5 years now. It's frustrating. VERY.
But, it'll get to us eventually.