Have you a link we can look at ?
I can't help raising an eyebrow at the fact you intend using frames - it's one of the fundamental must-not-do rules of good web design.
Many of the old problems frames faced in terms of browser interpretations have long since disappeared but they still fall short in many areas of accessibility, searchability and accurate display on many handheld devices. There is also an additional requirement for refresh code to be embedded into your main content pages, so that anyone who accidentally bookmarks a content page and not the surrounding frameset will have that page automatically reload with the frameset intact. Not doing this runs the very real risk that someone can visit your site from a bookmark and only see some content, with no navigation panel, header or footer.
My first suggestion would be for you to ditch frames entirely - using includes and/or CSS offers greater flexibility than frames for navigation structures, headers and footers et al.
If you're dead set on frames then a link to your problem page would probably point us in the right direction.
I imagine you haven't targeted the pages properly that make up your page layout. If your main frameset page is index.html, it could contain:
<frameset rows="*" cols="80,*" frameborder="no" border="0" framespacing="0">
<frame src="left_panel.html" name="leftFrame" scrolling="No" noresize="noresize" id="leftFrame" title="leftFrame" />
<frameset rows="80,*" frameborder="no" border="0" framespacing="0">
<frame src="header.html" name="topFrame" scrolling="No" noresize="noresize" id="topFrame" title="topFrame" />
<frame src="main_content_area.html" name="mainFrame" id="mainFrame" title="mainFrame" />
The above was created in Dreamweaver in about 30 seconds, and the only thing I changed was the name of the referenced pages that make up each piece of the whole (left_panel.html, header.html and main_content_area.html respectively).
Managing a frames site can become a real chore over time, so I'd urge you to think very carefully before investing a lot of time and effort into something with so many inherent issues.