hum, I've downloaded a few of those modules, but I haven't yet found any '~~' in any of them:
xmath@quoose cpan/build$ ls
xmath@quoose cpan/build$ grep -rs '~~' *
Am I missing something, or did you do something wrong with the search?
addendum: oh, this is a list of all modules checked? If so, I misunderstood. (a list of modules where you found ~~ would have been more useful to save downloading those which don't :-)