Note that this bug is found in Bricksmith, too. Confuses me all the time when parts seem to disappear behind the transparent canopy of starfighter models. Basically, through transparent parts you can only see parts that are specified earlier in the file; the transparent part seems "opaque" to parts specified after it in the file. (I reported this to Allen in 2008, who indicated that this is a consequence of how OpenGL computes transparency.)
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