you have set the "min-height" to "2em", but this leaves you at the mercy of the Moodle theme to decide how high a single "em" unit is. Obviously for the the themes based on Bootstrap3, the "em" unit is too small for your purposes.
If you wish to stick with the themes based on Bootstrap 3, I suggest you set the "min-height" on this JMatch exercise to "48px". It will then display as in the attached screenshot, which is using the Bootstrap 3 theme on Moodle 2.8.
I could not reproduce the orphaned white box that appears in your initial screenshot. I guess this comes from html that you have inserted in the top of the document using the settings for the theme.