I have been experiencing the exact same problems here.
Over the past three months, this has been occurring to me.
I am running DTV and Analogue foxtel using the reg hack, so I have the first 99 channels ( i think ) reserved for my digital FTA card, and any numbers above that should point to the analogue card with foxtel running through it.
However, every now and then when the guide updates, one of my free to air channels becomes a foxtel channel, ie, when I press channel 7, the MCE box attempts to blast some random number into the foxtel box and kicks over to the foxtel card
Im thinking of moving to freeepg cause I believe it's an issue with bladerunner or something involved in the guide process, but FreeEPG atm doesnt have FTA channels in the foxtel premium package!