I have been struggling for weeks (literally) with this problem. On the single post page of my Wordpress site (e.g. www.natmd.com/tai-chi-and-parkinsons-disease/) I cannot get the sidebar - and now the post area element also - to align properly. If I manually adjust the borders/margins it causes the elements on the home page and category pages to slip upwards and sideways. I believe this might have happened because I removed the search box and lengthened the space for the submenu, but I cannot see where I may have made a misktake there. I am not experienced with web design (I know, some people would say I shouldn't mess with code then, but I can't help it, I prefer to learn as I go) and I am even having a hard time understanding validation and fixing the errors I find there. Can someone come to the rescue?
If I understand your problem... Its a css error.. the top box (postarea) has margin: 0px 0px 10px 0px; and the other boxes (adsense, comments) have margin: 0px 0px 10px 10px; Set them all the same?