I'm having the same problem. Media files, attachments and theme files get uploaded successfully but when i try to upload the custom files i get the "source file not found" error.
I'm using Wordpress with it's own directory and I believe the bug is this one:
* When it searches for files it places the wp directory in the path correctly like this:
wpdirectory/wp-content/etc/etc
This way the total number of files is displayed correctly.
* But when i click the Start (upload) button, for some reason it tries to upload the files without using the WP directory in the path like this:
wp-content/etc/etc
Can anyone help? I've been trying to make it work for hours.
Thanks