I'm uploading three files:
spinner33-main_page.gif is matched to the main page top bar color.
spinner6b-upload_dialog.gif is matched to the #6B6B6B bar in the upload dialog (its color is #666 but also 50% transparent).
spinner55-compromise.gif has been exported on a #555555 matte, and looks average in both dialogs.
Ideally each page would use the "right" GIF, but you could also just replace images/spinner.gif with spinner55-compromise.gif for an okayish presentation (it will look a bit fuzzy in the main page and have a slight dark fringe in the upload dialog).
For future reference: What I did was download the Photoshop CS5 30-day trial, add an "invert" filter layer to the Panic PSD to make it whiter instead of blacker, and then set the matte color while saving via the Save for Web dialog.