viper 5701 remote problem

I have a viper 5701 installed in my 02 Jetta. It came in the car when I bought it, so I have no idea what exactly all was installed with the system. About a month ago I bought 2 additional remotes for the system - a one-way and a two-way - and programmed them both myself. First off, I will say that I suspect that I have two separate issues. The first issue is that the two-way remote that came programmed with the car first failed to open the trunk a couple of days ago. I figured the battery was low and changed it. That fixed the trunk problem, but now whenever the remote locks the car, the car chirps once as it is supposed to, and then again a second later. Then the remote makes a low-pitched chirp and the ghost lights next to the lock button and the function button light up for a second. The second issue is with the two-way remote that I programmed myself. It has the same problem as the first remote for locking. For unlocking, the car will chirp an additional time and then the remote will chirp and blink the light next to the function button 8 times in groups of 2. Both remotes work when I push the buttons, but they obviously think there is something wrong and I'd like to know what it is and how to fix it.

First thought, maybe the door trigger error was prorammed of by a bitwriter whilst they were using one remote, now with the addition on a new remote the setting is changed when you use that remote, also a second chirp when you arm indicates door, hood or trunk ajar.

It's a door trigger bypass problem, download the install manual from this site, it should give you the answer.

Thanks for the help on problem one. The hood was down but the catch hadn't fully engaged - problem solved. Still have the problem with the two-way remote I programmed beeping 8 times in a row after confirming that the command was received (sounds like "dingdong" almost). I mis-typed the first time around - the dingdong part is why I said groups of two, but it actually makes 8 dingdongs. I appreciate the help.