Reno - 2:01 am on Jul 15, 2010 (gmt 0)
If your "main menu" is now on all article pages, and is more than a link or two, then I reckon that is the problem.
I understand the complexity of this situation, but to think that simply putting a "main menu" on primary pages can cause this much havoc to an older well established site is very scary and drives home the point made many times in this thread about treading lightly when deciding on large scale changes. The evidence presented by flicky only hardens my resolve to not upset an apple cart that is holding the apples just fine and is attracting apple eaters on a regular basis. Sorry -- it's just too risky.