Nav links problem. Probably.

Links to categories are in flash. But articles linked from home page so...?

[Miamacs]

Happy new year everyone!
My first post here, I'm so honored. Have been reading the forum for some time now.

Our site is about 3 and a half years old.
Not much competition, it's a magazine of a niche where sadly no real money is around. No. 1 competitor is selling its web site as I type this... *grin*

But it's a fun thing to have, and it does well in Google. Apparently 60-70% of all visitors come from Google and land on the articles. We discovered this about a year into making it, it wasn't really aimed at Google.

Site structure is the following: Homepage, categories ( 3 main/broad and 7 subcategories but they're same level, and the broad ones are but the merged duplicates of those they summarize ), articles listed on category pages ( and the subcategory page as well ), and the table of contents on the homepage, which links directly to the articles one by one.

Or better put, it would be like this if the site nav links weren't all in flash.

But since they are, they're not followed, and Google seems to be picking up the table of contents links instead, bypassing the categories and going straight at the articles from the homepage. There are no sitewide text nav links to the category pages, the one that are indexed were crawled from either inbounds or age old residual links.

Homepage has a pagerank of 5, articles range from 4 to 3, older ones have 2,1,0. ( I think this has to do with the fact that the older they are, the lower their link is on the home page. ) None are supplemental. Category pages have a big white 0 for their pagerank, and aside the two that were indexed by chance, none is in Google.

What do you think, should I leave it as it is?
I kind of recall a certain wisdom on here that don't fix what ain't broken, yet I also feel like as if this was a potential pitfall. But that might be just the usual paranoia?

There's the problem of the category pages having but the same content of their subs copied together, so even if we were to rework the navigation this would need some tweaking. Also the homepage links to the articles with their titles as the link text, while these category pages have anchor texts such as "clickedy click here", which obviously wouldn't help much with relevance.