It originated in WW1, long before the Flak 36 was thought of, and meant any sort of AA.
And why ack ack? Because the British Army phonetic alphabet of the time went "A for Ack, B for Beer, ..., Y for Yorker, Z for Zebra". This sounds rather like the RAF alphabet of WW2 but wasn't quite the seem: differences included M for Emma (so Pip Emma = After noon) rather than Monkey/Mother and G for Gee rather than George.
Somewhat more tedious detail to be found here: http://en.wikipedia.org/wiki/RAF_phonetic_alphabet
P.S. The Navy did things differently. Their A was for Apple. But they were both wrong. As any fule kno, A is for Horses.