I have three live sites that work fine - I see the files on my server and front-end and admin working OK. These sites are visible in manage sites option in JMS Site Manager - however in the tools menu these sites and their shared slave site are not visible.
The template I used is visible in Template menu.

Perhaps you have define website with an "infinite" loop.
I means that you create a website using a Jms Template that is defined on itself or something like that.
In the JMS tools, when it detects a slave definition that create loop (website created based on itself) - it stop the analysis and you could have Jms Tools that does not display everything.

So recheck the slave site definition and the "template" that they are using.