[imadthegreat]

I have a strange case. Here is the sequence of what happened.

1. I worked for Composite Software until May 2013. Taxes were withheld from salary I received and reflected on W2 at the end of year. So far hunky dori.
2. I had incentive stock options at Composite Software. Just before I resigned, I exercised my options and bought whatever I was eligible for.
3. Less than a month after I left Composite, Cisco acquires Composite.
4. Before the end of year 2013, I surrender my stock certificate and get some money for my shares (some money was held in escrow acocunt- but don't worry about that now).
5. This income went unreported. Cisco did not reported it.
6. No, I didn't cheated. Very honestly I reported the check I received minus option strike price I paid to Composite to acquire my stocks.
7. Since, this was short term gain, my income was taxed at regular income tax bracket I fall in.
8. I paid my taxes. Life was good and peaceful.
9. In early 2015, Cisco realized that they should report the stock payment on wages and salary and created a new W2C and reported to IRS my ISO income.
10. IRS says that this new income is reported to them which I didn't include in my 1040 and I owe them additional $2100 in taxes plus 3% interest.
11. Now, Cisco is willing to give me a letter (which apparently they already sent), that says its ISO income. If I give that to IRS, they will get off my back. Again, hunky dori.

12. Now, here is the problem. Cisco is reporting some amount X which is less than half of what I received and I already reported. May be I don't owe taxes on all of it. In that case, should I submit a corrected 1040 and this time eliminate anything that was not reported and pay taxes on reported income? That way I can probably get $2500 back instead of owing them $2100.

Why do you think Cisco is reporting less than the check they paid me for my stocks (I have asked them this question but waiting for their reply)?

[AtlantaTaxExpert]

The ISO you received is considered to be COMPENSATION, which is liable for FICA (Social Security and Medicare) taxes as well state, local and federal income taxes.

You probably reported the option sales only as a stock transaction, and probably reported it incorrectly. Since the option is reported as compensation on W-2, if you immediately sell the stock, the proceeds and basis are generally the same, so ZERO capital gain or perhaps a small loss because the transaction fees are added to the basis.

STRONGLY recommend you get professional help to fix this problem. Your 2013 tax return needs to be amended to fix this errors in the W-2 reporting and to correct the Schedule D/Form 8949 entries.