Just so long you adjusted them with the front wheel fully seated in the fork dropouts, you should have no problem.
A trick is not to lock your front skewer until you put the bike on the ground and gently bounce it to seat the front axle. Then while its on the ground and you have a little weight on the frame, lock the skewer and then set the brakes to the rim as it sits. From now on, you should be able to always seat your wheel firmly and when you lock the skewer down, the wheel and tire should always line up in the same spot. And make sure to always have the skewer handle be on the non-drive side of the bike as is the rear skewer.