Anyone Else - 2011 1040 Efiled, Later IRS Says Didn't File?

[taxref]

This is not really a tax question; rather, its just something I'm curious about.  

I efiled about 85 returns in 2012 for 2011.  Those were a mixture of 1040s, 1120s, and 1120Ss,  I received an approved ack for every return efiled. 

Of the 1040s, 2 different clients received a notice in the Spring of 2013 saying they did not file for 2011.  In both cases, the clients had received their 2011 refunds in a timely manner.  One of the notices was addressed only to a spouse, while the other was addressed to both the taxpayer and spouse.  I was able to resolve one of the returns quickly, but for the other one I might have to go to the TAO.  

Anyway, I think that 2 IRS computer errors out of the small amount of returns I filed is quite a high percentage.  Have any other preparers on Tax Talk had this situation come up?  

[mwcpa]

I have not seen this.....

I find it odd that they got "refunds" and still IRS thinks the forms were not filed for the year in question....

What service center were the letters generated from?

[taxref]

I would have to dig a bit to find the service center for the resolved return, but for the ongoing problem the letters came out of Austin.  

The second round of correspondence has just been sent out to them.  That included a signed copy of the 1040, as they wouldn't accept the first copy, which only had the electronic signatures.  I have warned the clients not to cash (luckily, they didn't do direct deposit) any extra refund check they may receive.