On ZebraDesigner driver's side
Be sure to have configured the correct media parameters, according to the actual size of your labels.
In the ZDesigner Driver v5
Go to Printing Preferences > Options tab and adjust the media size on Size.
In the ZDesigner Driver v10
Go to Printing Preferences > Page Setup tab and adjust the media size on Media Settings.

On your PDF client's side
Be sure to check the option that fits the PDF file to paper size, the name may vary according to the client you are using. You can see 2 examples below:
In Google Chrome

In Adobe Reader

Helpful Information: