Would you mind share your form with me?
You can share your form by doing the following:
1. Click on “Design tab” on the top left corner.
2. Click on the “Share” icon on the bottom left corner.
3. Click on “Add Collaborator” on the popup menu.
4. Enter email@example.com under “People to share with”.
5. In the Message edit box, type "Issue with checkboxes"
6. Click the “Share” button on the bottom right of the dialog.
What happens if you zoom in? Is there any difference when you print?
When I zoom in the boxes are OK. In prints it looks like some boxes are sharper than others, so I think the problem occurs there too. Is there a way to make the boxes look all the same when viewing the pdf in 100%?
If you're using a border color for the check boxes, there's not a lot you can do, but turning off the "enhance thin lines" preference will probably make it better if it's currently on (see below). At the smaller zooms you will see this and it's affected by the resolution preference: Edit > Preferences > Page Display > Resolution. Changing this setting won't fix this behavior, but you should set it to match the monitor you're using.
If the boxes are part of the underlying page contents and you're not using a border color for the check boxes (though it doesn't sound like this is the case for you), depending on how the boxes are represented in the PDF (text, vector, or image), adjusting various display preferences in Acrobat/Reader may have an effect. I'm thinking of things like:
Edit > Preferences > Page Display > Enhance Thin Lines (affects vectors only, turn off)
Edit > Preferences > Page Display > Smooth Line Are (affects vectors only, probably won't make a difference)
Edit > Preferences > Page Display > Smooth Text (affects text only, probably not the problem)
Edit > Preferences > Page Display > Smooth Images
Without knowing how the boxes are represented in the PDF, it's hard to say what you can do about it, but I almost always use a character from a font for my check boxes to better avoid issues like this.
There is one thing that you can try. You need to modify the original PDF that you used for importing and import it again.
1. Make a copy of the PDF for backup.
2. Open the PDF
3. Switch your PDF to Editing mode by clicking Forms | Edit on the right pane
4. Select all the checkboxes
5. Right click on one of the boxes and select "Set Fields to Same Size" and then "Both"
6. Unselect all your checkboxes
7. Select checkboxes one row at a time.
8. Right click on one of the boxes and select "Align, Distribute or Center" and then "Align top"
9. Repeat steps 7 and 8 for all the rows that have check boxes
10. Import the changed PDF into FormsCentral
11. Download the "submission enabled" PDF and check your result.
Hope this works for you.