Technically speaking, this behavior is by design. The problem obviously comes from having two RadWindowManagers using different skins on the same page. One is your "regular" window manager, and the other is created by the RadFileExporer.
The radopen, radalert
methods use the last registered RadWindowManager on the page.
To prevent this behavior from happening would require changing both the server and client code of RadWindowManager. We logged it for fixing, but for the time being there is no perfect workaround.
One approach is to set the same skin to both controls.
The other approach would be to reverse the order of the RadWindowManager and RadFileExplorer on the page - in that manner the explorer popups will start using the Default
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