a strange problem regarding popup JDialogs/Windows

I have a complex program that reads Gerber files and renders a board
layout on a JPanel using java2d drawing functions. That works fine but
I'm bumping into a problem where some boards cause any future dialogs
in my program not to paint. This same phenomenon occurs with ALL
boards i zoom them to be too small, but there is no standard "too
small" it's different in each case. The behavior of other dialogs and
Panels besides the board layout is as such: they appear and all their
componenets are present, but they are covered in grey and the
components only SHOW if i select them. If i zoom any board in enough
so it's blown up enough, this stops happening.
So my question, is there some common problem with the 2DGraphics in
Java and drawing small objects that would cause this and I am just
unaware? Has anyone ever had a similar problem with dialog blocking,
and if so how did you solve it? I'd post code but there tens of
thousands of lines and i have no idea where this bug is originating

.