knocking at start

I'm asking this question for my father, since he has the complete opposite car as me, but is having an issue.

We tried a new code scanner on his car, because his check engine light would come on. We got that code, and so we cleared the computers trouble codes. (the engine never had a problem, it was a false code).

Upon starting the car after clearing it, when my father starts the car, he hears a knocking sound for 2 seconds, the car sounds like a diesel truck. After 2 seconds, you hear it fade away quickly, and the car drives fine. I tried clearing the codes again (even though there was no trouble light), and the sound went away immediately.. Then, 2 days later, it came back.

What can cause this? I assume it's the computer since it started since clearing the trouble light codes.

1995 Police Interceptor Crown Vic

it has OBD-II on it...

The car now makes 5 long beeps, while my father is driving it.. The dashboard doesn't indicate anything at all, except 5 long beeps..