You are not alone. I had the same problem many times in the past. No secondary questioning, though. I also encountered many INS officers curse at the machine for its lack of accurate information. One officer told me it had to do with US Customs and not INS. I haven't had any problems lately. I do about 18 international trips a year.
Another officer told me to submit a FOIA form to find out what was causing the flag.
Once my wife was heavily questioned because a person with a similar name was wanted by the IRS in NY. She never lived or workd in NY.
Go figure.
J.