The debugging requires an access to your schematic, but it may be not acceptable to ask you to upload your schematic to this public community.
So, please open a service request to Freescale technical support and attach your schematic to that service request.
Please do not forget to add a reference to this community topic.
In the mean time I suggest switching to default HRCW by pulling RSTCONF high (if your design allows that) and check if the problem remains (no further assertions of cs0 occurs after HRESET deassertion)
Also please confirm that you are aware about device errata G12 and have recommended workaround implemented.
Link to device errata:
http://cache.freescale.com/files/32bit/doc/errata/MPC8272CE.pdf