I'm seeing the following issue quite consistently throughout several of my websites:
Popup dialogs are sporting a transparent background, accross all browsers, making them unusable or hard to read.
I found only one issue that has significant discussion on this, http://drupal.org/node/936120, and it relates to the date module. However, it appears that in my case and with other Drupallers that this symptom is not 1 - module specific, 2 not a theming issue.
The only thing that may be specific to my case is that I use Panels everywhere (litteraly, as a matter of fact).
I have all the necessary JQuery modules like Jquery update solidly in place. Using version 1.7.
I experience this issue with Disqus comments (where if you hit the 'like' button, a dialog opens to share to facebook and Twitter). I'm also seeing this with the Custom Search module, where search options can be set to display in a popup dialog when you click the search bar.
No matter what theme I use, this persists.
Any thoughts, experiences, hopes :)?