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The suggested spacing for JRadioButton and JCheckBox appears to default to zero on Mac OS X, whether placed horizontally or vertically. To reproduce, create a new form and place four radio buttons in a square configuration, following the form builders positioning guidelines. This will results with no spacing at all between the components. The same will happen with JCheckBoxes. One can obviously work around the problem by adjusting the spacing by hand, but obviously this solution has, to say the least, a lot of drawbacks. I believe this issue may be the root cause of issue #92617 - if you preview the form in a different look and feel using the default zero spacing, you get the crazy IDE behavior described in that issue. If you set all of the spacing by hand (using "Space Around Components") so that none of the spacing reads Default, than the behavior in #92617 does not happen. If ANY of the spacing is left Default, then you get wrong layout along whatever dimension was left set at Default. I discovered this when trying out NetBeans 5.5 on OS X, and tried the 6.0 m7 milestone, and the problem is still there. The bug does not appear to exist on Linux.
This is caused by the fact that we set the border and margin of checkboxes and radiobuttons to zero. The AquaLayoutStyle does not take this into account - it provides gap that would be fine for the default border/margin. We will consider to stop modifying the border/margin of radiobutons and checkboxes, however it makes the layout look a lot uglier on Windows. But modifying causes problems in other look and feels - e.g. this spacing issue in Aqua, or the focus rectangle issue on Metal (see issue 97255). So probably we should make sure that at least spacing is fixed for radiobuttons and checkboxes in their default config on Windows and give up on the proper parallel aligning. Meanwhile, a probably better workaround for you is to set border and margin properties to default, rather than trying to set explicit spaces between the components. BTW Issue 92617 is most likely caused by bug 46 in AquaLayoutStyle, just exposed due to setting the empty border to the checkboxes/radiobuttons. It can be fixed separately.
Fixed with issue 74522 as described - don't set zero border and margin to checkboxes and radiobuttons anymore. *** This issue has been marked as a duplicate of 74522 ***