You are using Mac right? When you delete files from the flash drive on a Mac do you also empty the trash? If not Mac will not actually free the space that was used by the file you deleted.
Here is what you can try. Make sure the files are copied out of secure access 1.0 and are on your computer HDD. Once that is done open disk utility and erase the USB flash drive. if you ahve single files larger than 4GB make sure you use exFAT for the file system. Once the flash drive is completely empty download and install secure access 2.0 and import the files from your computer HDD to secureaccess 2.0. Once you have verified all files are now in secureaccess 2.0 you can delete them from the computer if you want to.
