Dupe Content Filter and "Home" link on subdomain

Did I get caught in the duplicate content filter?

[BushMackel]

I usually spend most of my time on the adsense boards, but last night I was doing some reading in google search and I found a sticky about the duplicate content filter. The part I'm talking about in particular is :

Duplicate Content Filter - incorrect linking
Applied: when internal links are incorrectly applied to "/index.htm" , "/default.htm" when they should all point to "/"
Effect: Unlikely to be indexed, badly suppressed results , PR applied to wrong or duplicate pages.
Time to restore : 2-3 months from when fix is applied

In one of my subdomains that has original content, decent inbound links and outbound links, I found something I did on the nav footer a while ago. I was linking to the subdomain's index.html page on it's index.html page and deeper pages in the subdomain like this :

<a href = "http://widgetville.widgets.com/index.html">Home</a>

After some reading on the Google Search boards, it looks like I should've been linking all the while like this...

<a href = "/">Home</a>

I bring this up because I can't find my subdomain on google, I'm apart of google sitemaps, (no probs there), and like I said, I'm getting crawled, have good inbound and outbound etc...Have I been caught by the dupe content filter?

[tedster]

I would suggest this form, used in every case:
<a href = "http://widgetville.widgets.com/">Home</a>

[BushMackel]

Thanks. Do you think that's why google hasn't been picking up my page?