How to tell if you have a bypass module

I recently purchased a 2001 Eddie Bauer Expedition.  Of course, I was spooked the first time I locked the truck and about 5 seconds later it cranked up again.  I discovered it has a RKE system on it.  I took it to a car audio shop and they said it's a cheap off brand.  The problem is I am no longer able to make the truck go into programming  mode so I can't program my RKE remotes (the truck didn't come with any, so I bought some from ford).  I wanted to tell if the RKE someone has installed on the truck has a by pass installed which is preventing my factory module from entering programming mode.  Anyone have any tips of how I can tell this? 

Thanks

I'm not the most familiar with alarm installs, but I've read somewhere that if your car has a factory remote keyless entry/alarm system, if they put on an aftermarket remote start or alarm system, they will bypass the factory alarm/rke system.  I'm not sure?  Is this done with wiring or is there an actual module to do this?

For my model Expedition, I'm suppossed to turn the ignition from off to on 8 times and on the 8th time, it should automatically lock and then unlock the doors to signify it's in programming mode.  Even at the dealership, when they do this procedure it never enters programming mode.  They think it's either bypassed or the rke brain is messed up from the remote start which was put on. 

Unplug your aftermarket RKE brain and than try to program your factory remotes