Both are grammatically correct. 1 is very clear and 2 should be changed unless you have context making things obvious.
With 1, it's redundant to say "A" system and "A" programme, but not so redundant that it's jarring - a reader/listener would gather that you are trying to make it clear that you did both things related to "A".
With 2, I would change it to:
Participated in project work on the "A" system and created its programme.
unless its obvious by way of context to the reader/listener that you could work on the "A" system and also create "A"'s program. If in doubt, change it.