Quaqua Look and Feel

Matisse is the name of the 'free form' editor in the NetBeans IDE.

Matisse allows to quickly create complex layouts which automatically take the preferred spacings of the current look and feel into account.

Matisse removes borders and margins from JRadioButtons and JCheckBoxes. (see NetBeans Issue #74522).
This breaks the alignment of the Quaqua component UI's and causes parts of the button artwork being cut off.
Matisse only supports RELATED and PARENT component spacings, all other spacings (UNRELATED and INDENT) are explicitly specified in pixels.
Layouts that contain spacings based on pixel values, which will only look correct for the look and feel the layout was created with. Most importantly, a layout created for Apple's Aqua Look and Feel will look different when run with the Quaqua Look and Feel.
Matisse organizes the GroupLayout into horizontal and vertical groups, without taking the logical structure of the components into account.
This may cause irregular spacings between components.

After adding a JRadioButton or a JCheckBox a the form, change its border and its margins to the default value.
Alternatively, set the System property Quaqua.enforceVisualMargin=true before creating a QuaquaLookAndFeel object.
After you have laid out all components on the form, take a look at the generated code in method initComponents. If the code contains absolute gap values in Pixels, change the layout until all values are based on logical values. If your layout contains indentations, create a copy of method initComponents, and code the indentations manually (see GroupLayout on how to do this). Put the original initComponents method into /* */ comments.
After you have laid out all components on the form, take a look at the generated code in method initComponents. If the GroupLayout groups do not match the logical structure of the components, create a copy of method initComponents, and rearrange the groups manually. Put the original initComponents method into /* */ comments.