The Crankshaft Position (CKP) sensor sends pulses to the PCM as the reluctor wheel teeth rotate past the CKP sensor. The PCM uses the CKP pulses to synchronize the ignition and fuel injector operation, and to time the interval between each CKP pulse. The PCM determines when an excessive change in crankshaft speed occurs by comparing each new time interval with the previous interval. A misfire causes an unexpected change in the crankshaft speed. A certain amount of acceleration/deceleration is expected between each firing stroke, but if the crankshaft speed changes more than an expected amount, the PCM interprets this as a misfire. The interval between CKP sensor pulses is extremely small. At high engine speeds, slight variations in the following components make misfire detection difficult:

Crankshaft
Reluctor wheel
CKP sensor

The PCM learns variations during the Crankshaft Position System Variation Learning Procedure. The PCM compensates for these variations when performing detect misfire calculations. Only a bi-directional scan tool can command the PCM to perform the Crankshaft Position System Variation Learning Procedure again. Perform the learning procedure after the following actions:

A PCM replacement
Any operation or repair involving the crankshaft, the CKP sensor, or the CKP sensor to reluctor wheel gap relationship.
An engine replacement.
The ignition switch is in the ON position until the battery is drained

It did this because it was falsely detecting misfires... the PCM had bad CASE relearn data, so every crank event looked like a misfire.

The PCM always knows the crank position... the CKP reluctor wheel is fixed to the crank, it can never lose its position;

the CASE relearn measures the crank's rate of deceleration on fuel cutoff and stores it for future reference... by comparing each crank event against this the PCM can detect misfires.