Two issues have been resolved with this fix.
First issue - organization - replies in forums were set to display newest first, but if you replied to another reply it would be placed beneath it in a "thread". This is why some replies were showing up above others - as fil pointed out it depended on which Reply button you clicked on. I switched us from threaded to flat, and oldest comment first. This way you can read and scroll down - as opposed to having to scroll all the way to the bottom first and read each post, scrolling up for the newer one.
Second issue - as a thread progressed it grew narrower and narrower within the confines of the site layout, which in my opinion made it more difficult to read. We are now using a flat layout instead of threaded - this prevents the replies from getting narrower.
Please let me know if there are any problems with this.
"What a waste it is...to lose one's mind...or not to have a mind...is being very wasteful." - George Bush Sr.