I guess this happened after I shortened the page length by adding "Read More" breakers in the posts. Now I have sidebar displayed way down the left side of the page, instead of the normal line-up with the top of the content.
This happened in the index page and I managed to shift the problem to Page 2 by reducing the number of posts on each page from the default 10 to 7.
I have tried a fresh install of WordPress and themes and the problem persists.
Any suggestions are appreciated.