Power Door Locks

I have a 99 Sub. The power door locks quit working. I thought it would be just a fuse but I have checked all the fuses and everything checks out okay. BUT they will work with the remote buttons (at least that’s what the wife says). It has an aftermarket remote engine start system that will also un-lock the doors. It seems strange to me that the remote will make un-lock the doors but the normal system does not. Anyone have this problem??