I'm not sure why you're getting such unpredictible behavior, but if you do a perldoc on MIME::Base64 and check out the examples, you'll see a couple of neat tricks. My favorite is the "if you have enough memory" option:

use MIME::Base64 qw(encode_base64);
local($/) = undef;  # slurp
print encode_base64(<STDIN>);
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Spud Zeppelin * spud@spudzeppelin.com