What backend does JSON use? JSON::PP or JSON::XS, or even Cpanel::JSON::XS or JSON::backportPP? What version?

Also, you probably want

my @keys = keys %urlparams;
#          ~~~~
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Otherwise, you're processing values, too.

Moreover, you probably want

         $input{$key} = HTML::Entities::encode($urlparams{$key});
         #                                      ~~~~~~~~~
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otherwise there's nothing to store.

Can you share a snippet that actually reproduces your problem? I tried to fix you sample and ran it under JSON::PP, JSON::XS, and Cpanel::JSON::XS, but there were no errors.