First, establish that you have a problem. Put your fly cutter in and see if it runs true or not, but make sure the slot isnt aligned with the pin hole or any burr might fall into the slot and mask the problem.
If you think there is a burr around the pin hole then yit should show up as a shiny spot. You might also try using a magic marker to black the shaft of your flycutter and then the burr will leave a shiny scratch on that.
If you fid that you do have a burr, use your dremel and remove the smallest amount possible to createa low spot instead of a hump. Don't try to chuck it up and turn it, it will almost certainly make things worse.