So, what were you using? Buttons? Checkboxes? From the description, it sounds like Checkboxes. In this case, open the PDF in Acrobat, switch to the form edit mode, select the checkbox(es), and display the properties. In the Appearance tab, you can set the border style and width, as well as the colors. Note that checkboxes have essentially 3 line widths (corresponding 1, 2, and 3 pt). Other values (0, 4 and higher) can be set using JavaScript, but may have unpredictible results. Now, if the appearance of the line is not "good enough", you could set the border to transparent, and scale the field so that the square when checked is positioned properly. That would use the line from the base document. However, you'd have to be very careful with positioning. Hope this can help.
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