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First of all: WebmasterWorld Google search [google.com]. Bookmark it, it's fast and it helps!
I wouldn't worry too much if I were you. If the domain is clean etc. it could be that enough time hasn't passed.
1. Do you have access to the logs for the site and if so has Googlebot hit the deeper pages?
2. Do you have some "deep links" from other sites pointing to your deeper pages?
I would have a look at your logs, bacause if Googlbot has been to the deeper pages and continues to visit them it is only a matter of time.
If not (well, regardless actually) I would try and get some deeper links to encourage the bots to get to that content.
HTH
mysite.com/content_folder/here.htm & one deeper:
No problem with that... I use a date based structure on one of my sites that goes
www.mysite.com/~maintopic/2004/07/subsidiary-info/file.html
Google will not be put off by the depth of *nesting*, it's whether it's possible to get there by following a reasonable number of *links*. For new pages I often list them on a "what's new" page that's one click from the home page - that gets 'em noticed...
DerekH