If you are seated at a table with a large party then yes, even with separate checks you will all be charged 18% on your portion of the bill.
Here is the policy from the tipping thread on the restaurant board...
Parties of 6 include everyone at the table, including children under 3 and infants. If you are dining with another group and paying separate, you are still subject to the 18% gratuity added to the bill. Each group at the table can get their own bill with their portion of the gratuity split out.