I agree with comments above, making a repeater is somewhat complex. With that said, you seem to be saying the repeater is working with mobiles. I'd triple check my programming. It is easy to make a mistake and have the handhelds talking and listening on the repeater output, which would work nearby as you would be talking HT to HT, but not far. If you did the same in a mobile, you might think it was going through the repeater, but get more range than with handhelds. So again, double check your programming.
Also, what duplexer are you using, how close together are TX and RX frequencies. The more technical information you provide the more folks may be able to help you. Obviously, it goes w/out saying that your company repeater must have FCC licensed frequencies, but I'm sure you know that.