Hello again perplexed,
As long as you had more taxes withheld from your paychecks than your actual tax liability was for the year, then the state cannot assess you with penalties and/or interest, since you paid in more than the total amount that was actually due.
It would be impossible for me to explain why they are still saying that you owe anything at all, however, I do know from personal experience that you could re-send this same information tomorrow, and depending on the examiner who reviews your information, you would likely get a totally different result.
It is sometimes very difficult to deal with these issues over the phone or by mail, and get them resolved in any timely manner. Because of that you may want to consider making a trip in person to a local
tax office in your area. I would take with you a copy of the return which you thought was filed and copies of all your W-2 forms and sit down with someone in person to show them these records.
Unless you somehow computed the wrong tax amount that was actually due for that year, if you really had enough taxes withheld to cover your liability for that year, then you should not owe any penalties. Unfortuntely, the only way to get this resolved will be through the Franchise Board, and it may take a personal trip to one of their offices if you are looking for the quickest resolution to this problem.
Thank you perplexed, and good luck to you in getting this resolved in a timely manner. Let me know if you have more questions. I am happy to help you with whatever I can.