I don't have a specific answer, but you should be able to sort this out by looking in the documentation. Two places to look in.
A pdf file called "fm12_instant_web_publish_en.pdf". This would have been included with your copy of FileMaker 12 client (and I think server). One about page 3-4, they talk about hosting for IWP and more relevant, starting on about page 33, several pages about working with FM Server Advanced and IWP. Guessing a bit, check the setting that says "Don't show this dB on IWP home page" that is referred to near the beginning of this document.
The other place is in the on-line help in FM server itself. There are several areas where IWP is discussed. Bring up the Help and search for "IWP".
Sorry I couldn't be more specific...but confident that you can find the answer.
Thanks Doug for the fast reply.
On all three databases IWP is managed by FMSA. I've read that the databases should be 'shared' either via FM Pro or the FMSA not both, and therefore the setting 'do not show on homepage' is off in the FM Pro Sharing menu item.
I'll read through the sections you mentioned, thank you.
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Agree that when on the FM server, all you need is to have the FMIWP extended privilege enabled in each file. There isn't an equivilent "Don't show" setting from the server perspective though. I am not able to test this currently, but something in the back of my mind says that this local FM client setting carries over with the file when it is hosted on a FM server.
Although I haven't tested this on my project management database I tested on a test db and you're absolutely right, somehow that setting is carried over to the uploaded server hosted file but you can't tell that that's the case by simply checking sharing, it appears not to be set.
When it's a little quieter I will remove the hosted file, change the setting and upload back to the server, reckon it'll work - will let you know.