Two similar domains - but one Homepage not appearing in Google

[Boston_SEO]

My homepage is not currently appearing in Google when I do a site:. It has a PR of 6, decent number of backlinks. I have indicated the correct url as the "preferred domain" in Google's Webmaster tools.

The likely issue is that we have a second site that is virtually identical to this site (one for patients/one for physicians type of thing). The url is different (i.e. example.com & example-other.com). This second site's homepage is appearing in Google.

The homepage uses Javascript to display the appropriate content (depending on which URL is being used).

Since search engines ignore Javascript, shouldn't they index both domains. If they do then is this a duplicate content issue where SE's are forced to decide which is the authentic homepage ... and for some reason they are selecting the second site as the authentic site?

Thanks for reading and your insight

[edited by: tedster at 4:12 am (utc) on Jan. 23, 2008]
[edit reason] switch to example.com - it can never be owned [/edit]

[tedster]

How do the two home pages compare with javascript turned off in your browser? If they're identical, there you have it.

[Boston_SEO]

Tried that and the most peculiar part is that the homepage that is not in google is the one that loads. The other homepage does not load with Javascript disabled.

[tedster]

Well, it sounds like you're going to need to get very precise here. Check the Google cache for the home page of both domains. Check through all the Webmaster Tools information for both.

Beware of any javascript redirects that Google might consider as "sneaky" - and any AJAX like functionality that does not give Google a url that preserves page-state.

Sounds like you're trying to leverage one database into parallel content for two different domains - and that just might not be do-able.