ok, my fellow liberal, I took a look at 2 pages..
the first thing that concerns me is this: http://validator.w3.org/check?uri=http://guntotingliberal.com/
252 errors, and while a lot of them _appear_ to be related to the use of tables, you have quite a few nested or improperly closed tags.
http://guntotingliberal.com/archives/80 contains 249 errors.
Here is what I would do if i were you:
For starters, you need to reduce those errors, signifigantly. Start at the front page, muddle through, and fix anything and everything you can.
Once you've done that:
go download a copy of beyond compare. Its a piece of software that allows you to compare 2 text files side by side for differences. It runs in windows. Its available here: http://www.scootersoftware.com/
Once you have that, save a copy of your front page from ie, or FF (it doesnt matter) and save a permalinked page (file || save as ).
Compare the 2 pages using beyond compare. (If it were me, I would temporarily change the posts displayed on your front page to ONE, so that youre displaying what you see on the permalink page)
What you will be able to see is what the browser sees (side by side)
There are several structural differences between your permalink pages and your main page, and they arent all related to the fact that you're including comments.
The first one starts right near the top after
</div> <!-- headerblock -->, for instance.
First things first though, you really need to reduce those errors. Anyone here that even attempts to guess at what might be causing your problem is prolly going to have to work all the more harder to definitively locate the problem because of the amount of errors.
Bad code in, bad code out, basically.