This rule in blocks.css:

#block-system-main .block-inner {
  margin: 0;
}

overrides the settings for the gutter in AT Responsive Panels (that is, the AT panels used by the Panels module). As a result, the same layout (say, AT Two column 66/33) looks different when it is used as a Gpanel and when it is used in a Panel.

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Priority:Normal» Major