Firstly, sorry if this has been mentioned already as I browsed through the thread rather quickly.
What version of workbench are you using with AmigaExplorer ?
I had plenty problems (games not booting, file transfer hanging up) when I used and old copy of WB 1.3 with AE and it turned out that the WB disk contained a ton of old viruses. I used a adf. image downloaded from somewhere, it's called something like viruschecker.adf to remove the viruses, and voilá, the transferred adf's worked perfectly
