OK, so you are definitely classified as on the semi-weekly deposit schedule since your lookback period 3rd quarter 2008 through 2nd quarter 2009 was over $50,000. This means that for wages paid on Saturday-Tuesday, deposit by the following Friday. For wages paid Wednesday-Friday, deposit by the following Wednesday. If you follow these rules, you'll always have at least 3 business days to deposit your payroll taxes timely. If you accumulate a tax liability of $100,000 or more on any day during a deposit period, you must deposit the tax by the next business day.
You indicated you normally deposit the taxes on the same date as your payroll. Therefore, if you do this, there should be no penalty. This CP notice may mean that you may be completing your Schedule B incorrectly. IRS uses the Schedule B information to determine if any deposits were late. Remember -deposit rules are based on the date wages are paid to your employees, not the date they earned the wages.
So for example, if employees were paid wages for the period ended 04/09/2010 on 04/16/2010. The payroll deposit is due by Wed. 04/21/2010. You want to be sure that you are using the 04/16/2010 date on Schedule B. Also, if you use EFTPS, you'll need to initiate the deposit one business day before the due date. So instead of Wed and Friday due dates, you'll need to initiate the payment in EFTPS by Tues. and Thurs. 8pm EDT.
Let me know if you have any questions.
Hope this helps,
Edited by JK_CPA on 6/2/2010 at 6:11 PM EST