As much as the Thesis Theme (or really framework) is supposed to be independent of upgrades to your plugins, a recent upgrade to WordPress 3.0 made significant enough changes that you may be experiencing the following error when trying to use the Custom File Editor for Thesis (I have 1.7 and experienced this, but older version will most likely also):

Fatal error: Call to undefined function use_codepress() in /directory/public_html/wp-content/themes/thesis_1.7/lib/admin/admin.php on line XX

A great solution has been outlined at the ThesisLab website. If you can edit the file directly from your FTP client do the following:

Comment out the line that calls for syntax highlighting by placing two forward slashes just before it. Example:

// if (use_codepress()) add_action('admin_print_footer_scripts', 'codepress_footer_js');

Essentially, until they update the code for the Thesis Theme, you will need to make the suggested modifications in order to use your built in custom file editor, and it will still not work as it did previously with the colored syntax highlighting.

All hope is not lost for editing your custom files if you want to wait it out for this upgrade. If you are using the custom file editor, chances are you are also well versed enough to use a file editor such as Dreamweaver or even a text editor with FTP access to change your files.

I do love the custom file editor for quick fixes though, can’t wait for a fix.