Virtex-5 bitstreams created with the -g Security:Level2 setting in 9.2.02i will not go through the startup sequence, even though DONE goes High. For Project Navigator users, the equivalent to the -g Security:Level2 setting is the "Security" property setting of "Disable Readback and Reconfiguration." The "Security" property can be found on the "Readback Options" page of the "Generate Programming File" process properties.
The other bitstream Security values: -g Security:None and -g Security:Level1 will not exhibit this problem. These are equivalent to the "None" and "Disable Readback" values, respectively, for Project Navigator users.
This issue has been fixed in sp3 of the software.
If Security settings are being used with a Virtex-5 device, please use 9.2.03i or later.