Ok, so the handbook indicates that the CPLD internal weak pull-ups are active in the unprogrammed state.
The signals connected to the CPLD pins will have a weak high applied to them. If an external device drives the signal on the CPLD, then it will over-ride the weak pull-up. If an external device is driven by the CPLD, then it will have a weak high applied, eg., an active low signal will be deasserted.
If you have a device signal that you would like a low on during power-on, then you need an external pull-down resistor on the signal, eg., 300-Ohms to ground. For example, the resetN signal on a controller that is controlled by the CPLD. If the CPLD is not programmed, then the external device will be held in reset.
I hope that is a little clearer.
Cheers,
Dave