check engine light

In Nov. '03 my the motor on my '97 Buick Park Avenue seized (the person who changed motors said it was because of a crease in the oil pan obviously caused in a previous incident prior to my buying the car; should have checked it out thoroughly in retrospect). Anyway, the motor installed was said to be '95 Olds (3.8 liter; same size as the original). My question is what would cause the check engine light to come on intermittently? This has occurred since Dec. '03. That is, it goes off after some long periods and comes on after hundreds of miles of driving ... making it wholly unreliable, I would guess. Could it be that the install of the replacement motor was not done correctly or could it be that the replacement motor is not wholly compatible with the Park Avenue circuitry? It would be greatly appreciated if anyone with insight can answer this.