Doesn't sound like the reg/rec issue, but don't rule anything out yet.

What error code is the flashing engine warning light showing with the ignition on? Count the long flashes and short flashes - the long ones equal the tens and the short ones the units. The sequence then repeats.

For example: _ _ . . _ _ . . _ _ . . is a code 22

If you can identify the error code it should help get to the bottom of things...

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