Q:

What could make Fancy Upload work in Firefox only after a succesful upload from IE on the same machine?

When uploading a file through a local instance of fancy upload with Firefox, the onComplete callback is fired. However when checking the file system, the upload has not completed.
If I then test the function in IE8, the upload works with no problem.
Then, after the IE upload, I test again in Firefox, now Firefox works with no problem.
Notes

The domain I am using is http://localhost
I am on PHP 5.2
I have the latest mootools installed and a lot of components from more, all with compatibility enabled.

A:

Sessions
The answer seems to lie in the way the different browsers handle session data via the Flash object.
In my upload method I use the session to handle some user data, however the session belongs to the flash object, not the user.
Then after the upload, IE is able to access the data added by the Flash object whereas Firefox cannot.
This results in some strange behavior. I have now modified my code to avoid using session data.

