There is a difference between ‘out of status’ and ‘unlawful presence’. For people who have a D/S on their I-94 (like people on F-1), “Nonimmigrants admitted to the United States for D/S begin accruing unlawful presence on the date USCIS finds a status violation while adjudicating a request for another immigration benefit, or on the date an immigration judge finds a status violation in the course of proceedings.”( Memorandum dated September 19, 1997, 96 Act #058).  

Legally, if you are not involved in OPT qualifying job (for regular OPT- any paid or unpaid work related to your major and for extended OPT- any paid job related to your major) for more than 90 days (120 for extended) you are out of status. However, when you try to change your status to something else, USCIS doesn’t look at your ‘payroll’ or ‘taxes’ to determine this. They just look at your SEVIS and if you have informed your school you are working, the school updates your SEVIS to indicate where you are working. They don’t know whether it is paid or unpaid. This means that as long as your SEVIS has a name of an employer, you can change your status without facing any problem.

The bottom line is don’t worry too much about this. Do your best to run your payroll but if not, don’t stress too much about it. It is highly unlikely that you will face any problems when you try to go back to school after the completion of the OPT period.   

If someone else knows more about this and I am incorrect, please correct me.