This was tested on the build dated 5/10/09.
I have more information though that may answer the question.
My assumption was that the control would automatically use the ~/UploaderTemp/ folder if it was created within the site. This is not the case, at least not on this particular client installation on Win2K8.
The uploaded files were probably getting put into the Windows temp folder. Since that folder lacks the same permissions as the site folder, the .MoveTo() function was moving a file with bad permissions assigned to it. Bad from an IIS perspective at least.
When we modified the control to force the uploadtemp folder to ~/UploaderTemp/, the .MoveTo() function moves the files correctly and with the correct permissions.