I accidentally used lc where I should have used uc, but you shouldn't get the behaviour you describe either way.

>type infile
hello h e l l o
bye b y e
bike b i k e

>perl -pe"s/(.)/uc($1)/e" infile > outfile

>type outfile
Hello h e l l o
Bye b y e
Bike b i k e
[download]

or

>type infile
hello h e l l o
bye b y e
bike b i k e

>type script.pl
while (<>) {
   s/(.)/uc($1)/e;
   print;
}

>perl script.pl infile > outfile

>type outfile
Hello h e l l o
Bye b y e
Bike b i k e
[download]

You must be doing something extra.