Problem with Popup vs. Create

Hi guys,
I have a problem - I have a page that I'm working on that has one CKEditor with CKFinder integration and one popup window that uses CKFinder to grab an image and put the url in the textbox.
I have BaseUrl defined as an "http://yoursite.com/content/" link and BaseDir defined as the physical path to the content folder "C:/blahblahblah/content/".
Everything works fine, I can upload using either method from CKEditor in the "Browse Server" popup, or using the "Upload" function. CKEditor is correctly inserting http paths. When I use the popup (same as the popup example, using finder.popup) I can correctly retrieve the path for an existing image, but when I click the upload button it just gives me an error. If I use a standalone instead of a popup (using finder.create instead of finder.popup) it works fine! But I need it to be a popup from a button to populate the field.
Is it possible that the popup uses the http path and the standalone (finder.create) uses the basedir?
Thanks for any help!
-Casey