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
Algorithm-Annotate-0.10       Algorithm-Evolutionary-0.53
Algorithm-BinPack-0.4         Algorithm-Evolve-0.03
Algorithm-Bucketizer-0.10     Algorithm-FastPermute-0.07
Algorithm-CheckDigits-0.38    Algorithm-FloodControl-1.00
Algorithm-ChooseSubsets-0.01  Algorithm-GDiffDelta-0.01
Algorithm-Cluster-1.28        Algorithm-GenerateSequence-0.02
Algorithm-Diff-1.1901         TransitiveClosure-1.4
Algorithm-Diff-Apply-0.2.3
xmath@quoose cpan/build$ grep -rs '~~' *
xmath@quoose cpan/build$
[download]

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 :-)