Check engine light problems

[91' loyale Sub]

I am experiencing a few problems with my 91' loyale wagon and was hoping some one could help. The first is my check engine light is coming on and the going off every time I accellerate. Is that the timing? The other thing is If the car is not warmed up my alternator will not charge the battery. WHen it kicks back down to around 1000 rpms after warming up it will charge. Is that normal? It seems it wont charge very well when the lights are either so I have not been driving at night. I recently replaced both the alternator and the battery. ANy thoughts?