Same problem has happened to a few people, including myself. Solution is to back down to 1.03, but the serial numbers could pose a problem there. Another solutuon is to use an alpha version of JEmplode with cloning support, or wait for empeg to release a new clone tool with the serial number problem fixed.

Personally, I am FTPing the data between the two units, and also cloning the scratch partition to save the plays data.