When you generate your Gerbers, what accuracy are you setting (2.3, 2.4, 2.5, etc)? You need to remember that those settings are in inches or mm, and specify the number of decimal places before and after the decimal point.
Since you're working in mils, and you're worrying about 0.5mil accuracy, you would need at least 2.4 or perhaps even 2.5. 5mils is 00.005in in 2.3 notation. Roundoff error could make that third decimal place vary +/- 1mil. 00.0050in (2.4 notation) would give you 0.5mil accuracy.