Thank you for your post.
I am unable to replicate the issue. This is what I have done:
1. Using FileMaker Pro 13.0v3 under Mac OS X 10.9.5, I create a database file Test.fmp12.
2. I created one Text field named Checkbox.
3. In Layout mode, I changed the Theme from Enlightened to Vibrant.
4. Still in Layout mode, I selected the Checkbox field and formatted it as a Checkbox set, creating and applying a value list that contains one custom value "1" (without quotes).
5. I sized the field so the "1" does not appear. The right side of the field is two or three pixels larger than the checkbox.
6. In Browse Mode, the "1" does not appear. I switched between all zoom levels from 25% up to 400%, and the "1" never appeared.
Let me know what I'm doing differently than you so I can try to replicate the issue.
Do you have any special graphic cards? What model Mac is being used? If another Mac is available, are you able to replicate on the other Mac?
Any other information you can provide to help me replicate the issue may be helpful.