I notice the same warning message, but in slightly different circumstances. Basically, it occurs when library A includes a tag file to library B where both libraries have been generated using 1.8.7 on Red Hat 5. Where both libraries are generated using Red Hat 6 (1.8.7), I do not see this warning message. However, though I see the warning message for the Red Hat 5 version, the resulting documentation appears to be the same as for the Red Hat 6 version, so I don't know what ill-effect it is having.
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