Netbeans does do really stupid things like that sometimes, and I generally get around them using either of these two methods:
First thing to try is to change the layout used. Try the Grid Bag Layout, or any of the others and see if you get better results.
If that doesn't work, then probably the easiest thing to do is to change stuff in the code. You will notice that Netbeans automatically adds a call to initComponents(); in the constructor (you have to switch to Code view from Design view). And if you look at initComponents, it will have a whole heap of auto-generated code to create the GUI. Do NOT edit this, because it's just a matter of time before Netbeans overwrites your changes. What I do is to create a new method initComponentsFix, and call that immeidtaely after initComponents in the constructor. In initComponentsFix, I would add the code to resize the component to the preferred size, and any other things you you want to fix.
BTW I empathise with you - Netbeans' GUI editor is still in need of much work. However, it's code auto-generation is still very useful, so I wouldn't recommend coding the GUI the good ol' fashioned way. That's why I'm advocating using it up until you start felling its limitations, after which you "take control".
There is also a third way, which I would not recommend, is to edit the file that Netbeans stores the Design view in, which is basically shares the same file name as your frame's class' source code, except with a .form extension.
This file is XML, and is pretty easy to edit. I don't recommend this because it is sorta going around the back door, but as a last resort, you can still try it.