I'm not sure why it's not working for you, but when I put in my 8gb verbatim usb thumbdrive formatted as FAT32 then the stock AcerMedia app reads the drive and shows the available files.
For example my movies show on the video page as a folder called usb_storage, except that only .avi files show up.
That's why I don't generally use AcerMedia but as splatoid said, 3rd party media players generally let you set the location(s) to scan for files.
HC3.2 apparently supports NTFS file format but I haven't tried it out, maybe that's the problem you're seeing? Do you know how your flash drive is formatted?