2001 sport trac remote start issue

hello everyone, im brand new to this site, im having problems, i got my remote start started installed today by a local shop, he programed it to work to my factory remote, but for some reason he said once the vehicle is running i cannot unlock it, which means as soon as i go to get in the car i cant use the fob. only by putting my key in the dr, its annoying, he said something about cutting a wire so when the vehicle is running it will disable this, also due to not being able to unlock the door i cannot shut it off because the lock button will not work. which is annoying because if i change my mind about going out i have to still walk to the car and hit the brake pedal. heres a bit of info on the vehicle,

2001 sport trac
auto
has keyless remote unlock.lock,
power windows,

all factory.

if you can help that would be great, my email is jonnyboys14@hotmail.com or i will see how to respond using this system again thanks so much. Jon

Factory disarm is not going to fix this problem.  The problem is just as most Toyota factory keyless entry modules, when the vehicle is running, it assumes you are in the car and there is no reason for the keyless entry to work.  There should be a wire on the factory keyless that tells the module that the key is on.  I have no idea where the module is located, nor do I know for sure that there is a switched 12 volt wire on the module.  But if they can find the module and interrupt switched power going to it while the vehicle is remote started, this may fix your problem.

hell everyone i found the wire, it was under the dash behind the airbag on the passengers side, its a red and black, or red and tan wire i believe, i pined it out and tested it. just wanted to say thank you to everyone who helped out. Thanks ! Jon