iMPACT does not allow JTAG operations on devices directly preceding a XCCACE (System ACE CF) device. However, iMPACT does correctly identify the entire chain and allow operations on devices not directly preceding XCCACE in the JTAG chain.
To work around this issue, run iMPACT in batch mode.
This problem has been fixed in the latest 6.2i Service Pack available at:
The first service pack containing the fix is 6.2i Service Pack 2.