Remote Update Cyclone III from EPCS

I am able to load in an Application configuration from a specified address in the EPCS, but after a certain time the device reconfigures itself with the Factory configuration (at address 0).

I am not using a Nios processor. Reconfiguration is controlled by an external processor and a simple state machine in the FPGA.

It seems that the first time I trigger the device to reconfigure itself with the Application configuration (address 30000) it will immediately reconfigure itself with the Factory configuration. On subsequent times it will keep the Application configuration for about a minute before reconfiguring itself with the Factory configuration.

It seems like it has something to do with the watchdog timer, but I have not enabled it. I have not been successful yet in reading back the status from the Remote Update circuit so I can't tell what caused the reconfiguration. I connected a signal that has a short pulse every millisecond up to the reset_timer line but that made it such that the FPGA would revert back to Factory configuration immediately every time I triggered a reconfiguration with the Application configuration.

Any ideas on what to look for would be appreciated.