Welcome to the forums!
When you've finished writing automation to a track make sure you switch the automation mode of the track to "read" or "off". If you leave it in touch or latch mode and you change nay parameters you may create automation values by mistake.
Is that what you mean?
Also, can you please list your system spec. e.g. OS version, exact Logic version and what mac you are using.
Finally, what parameters does Logic "do itself" - track volume levels? panning? And can you see the automation in track automation or hyper draw?