I'm using gpodder to manage podcast on Ubuntu machine (thinkpad laptop). When I transfer files to the phone I see the files on the phone sd card via ubuntu file manager, however, when I disconnect the phone and browse the files from android I don't see the file. Connecting the phone back to the machine and browsing to the appropriate folder, I don't see the files.
Are you unmounting the SD card before you unplug the phone? It sounds like the files are still buffered and you're disconnecting the device before they actually get written -- this is the main reason you need to sync/unmount drives before disconnecting them