Its actually never "%%%" per se.
You have to think through the process Keyboard Maestro will use. You double (%%) the percents you want to save. So for example the sequence of processing the string twice in a row goes from this:
%%ICUDateTime%%%Variable%fmt%%%
%ICUDateTime%dd/MM/yy%
19/04/16
If we code each percent as ①②③④⑤⑥ the doubling can be seen more clearly (I'd use colors, but Discourse does not support colors sensibly).
①①ICUDateTime②②③Variable④fmt⑤⑥⑥
①ICUDateTime②dd/MM/yy⑥
19/04/16
So you can see the percentage characters in the second process need to be doubled initially so they are preserved. That would be the ones labeled ①, ② and ⑥.
And initially within the format section, you have the variable expansion "%Variable%fmt%".