permalinks sidebar issues

my wordpress dashboard changes the structure of my permalinks with ease, and the haccess page is automatically changed as i altered the file’s permissions so it can be edited.

my blog works as normal but there’s a few discrepencies.

when i click a post title or sidebar link on the front page, everythings fine and the correct thing appears.

when i choose the category link on the ‘posted by x in x’ line beneath each blurb on the front page, all the sidebar links are incorrect.

is this a common problem and what can i do to change this?

also, does my rss feed change when my permalink structures do?

thanks.