Run

$line = "one % : thrre blblblb % 545334\n";
chomp($line);
print "$line valid\n";
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If you get

one % : thrre blblblb % 545334 
valid
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then someting is really wrong with your perl.

If you get,

one % : thrre blblblb % 545334 valid
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then chomp is working and my previous post stands. Answer the questions in my previous post if you want to find the problem. I've just added code snippets in that post to help you answer the questions.