XC18V02VQ44C Problem
IF the FPGA charge pump detects a low supply level, it shall restart the configuration load process setting "Init" low and so on.
1) I would try to ensure that the unexpected behaviour is not due to a failure in the supply (perhaps a bus conflict). It this happens then a configuration load shall de initated, so that just using a scope you could get that info.
2) If this do not occur, you should try to start thinking in having a problem, perhaps in your reset logic (external to the FPGA) or perhaps in the FPGA logic.
Are you using any evaluation IP? Sometimes these cores stalls after a time running. They have a counter hidden in the logic.