Hmm...I have a hard time imagining why that would be unless the joomla site somehow interacts with the vb site. You say it's not bridged and they have separate databases, but is the joomla site linking to or calling the vb site to get content?
I suppose it's somehow possible that the vb site is using excessive resources when it's closed. Do you have any way of looking at the processes running on your server?
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