I was told by VMware support, that this is a known problem with that Version of VMware converter. It will happen only for non-Operating System Disks if the transfer of the disk takes longer than one hour. Then the transfer times out. It will be fixed in a later major release of the converter.
Workaround is to copy only the OS-Disk with the converter, and to copy the other disks for example by SCP. Following the script I got from them, but I was not able to test it until now:
1. Convert disk 1 with VMware Converter
2. Log on to the ESX server you are moving to.
3. Determine the exact path to the VM. Example: /vmfs/volumes/UUID/myVM/
4. Log out
5. Log on to source ESX.
6. Navigate to the directory of the VM.
7. Copy the files of the remaining disks. Example:
scp disk3.vmdk
scp disk3-flat.vmdk
They can also be copied by FTP if it is enabled on the Firewall of the ESX (see Configuration Tab of the ESX Hosts).
8. In VC Edit the settings of the VM to make sure that disk 2, 3 and 4 are present.
If they are not, add existing disk and select disk 2, 3 and 4.