Chris,
Are you referring to IIS FTP?
If so, check if MSDTC service is still started on your target after the cloning.
XPe SP2 rel.notes:
a.. Cloning process (i.e. SysPrep) fails to restart MSDTC service when other services have started or are starting. Workaround:
issue the following commands after cloning completes, in order to restart MSDTC and IIS:
a.. msdtc -install -a
b.. msdtc -resetlog
c.. iisreset /restart