If you're really concerned

I would say find out politely. e.g say something like "I have no problem whatsoever to provide my passport, I am just curious why its needed this time. Is it because I am not a citizen yet?".
With the hightened security concerns, Dept of Homeland Security (DHS) has issued a more rigorous process for others to follow when it comes to verification of the employee's immgration and citizenship status. I wouldn't be surprised DOL has new procedures as to what data to collect from new employees for verification purpose. For aliens and nonresident aliens, passport data is the safest one to satisfy DHS. So I wouldn't worry about providing it.