There's nothing wrong with your program, and I can't replicate your problem. ( Also using ActiveState 5.10.0 )

>debug in.ico
-rcx
CX 0015
:
-d100 l15
0B12:0100  61 62 63 0D 64 65 66 0D-0A 67 68 69 0A 6A 6B 6C   abc.def..
+ghi.jkl
0B12:0110  0D 0A 0A 0D 0D                                    .....
-q

>c:\progs\perl5100\bin\perl 740238.pl

>fc /b in.ico out.ico
Comparing files in.ico and OUT.ICO
FC: no differences encountered

>debug out.ico
-rcx
CX 0015
:
-d100 l15
0B12:0100  61 62 63 0D 64 65 66 0D-0A 67 68 69 0A 6A 6B 6C   abc.def..
+ghi.jkl
0B12:0110  0D 0A 0A 0D 0D                                    .....
-q
[download]

I suspect some compatibility layer outside of Perl is messing with Perl's IO.