There seems to be some interaction in the string eval as this code does run.

cmpthese (-5,{
                me => "mymatch('AAAAA',2,['AAAAA','ATAAA',
                                          'ATCGA','ATCAA']);",
                jk => "amatch('AAAAA',['2'],('AAAAA','ATAAA',
                                             'ATCGA','ATCAA'));"
               });
[download]

While Joost is wrong (or I misunderstood him) about not being able it give Benchmark a string. His approach is normally the better one.

Update: The problem is that you are evaling the following strings:

mymatch(AAAAA,2,@arr)
amatch(AAAAA,['2'],AAAAA ATAAA ATCGA ATCAA)