Ryan asked that I post this to the forum. I completed a new install using the most recent upgrade for the WordPress install (beta) 3.0 using Scripts. I also uploaded the usual plugins that I typically use and have no issue with in earlier versions of WordPress.
I was getting a large blank white space in various postitons on both pages and posts for no appraent reason. Nothing was showing up in the html code. So there was nothing to delete. I called my hosting company to see if there were any known issues with this version of WordPress.
Support was reluctant to pursue any technical help other than server side issues (understandably). So, I fired off an email to Ryan and started to fiddle with disabling plugins to see what would happen.
Culprit was "All In One Adsense and YPN" by linewbie.com. That was the culprit. Turned that sucker off and all was one with the universe once again.
Ryan said he may deal with this in a future update of Flexibility.