Ok, I resolved this for me, but I think it is a pretty big bug in wordpress unless I am missing something.
I am working with a custom theme that I wrote.
There were two things that caused this problem, or maybe one thing depending on how you look at it.
I wanted my CSS Files for my theme to be in a css directory. So I moved the style.css file into the css directory. Then I changed the stylesheet entry in the database to reflect the themename/css and everything seemed to be ok. However, the next time I went to presentation it said I was using the default theme instead of my custom theme. So if I put my template files in the default theme folder they showed up, and it was still picking up the css I specified for my custom theme.
So finally I decided that I guess I can't have a css directory for my css files and moved style.css back into my themes root folder and selected my theme in presentation, and everything works ok now.
I don't understand why removing style.css from the theme root would make wordpress switch back to "Default" theme, especially since I told it in the database where the stylesheet was.
In any case hope this helps you level2d