Process p = Runtime.getRuntime().exec(
"c:/perl.exe"  C:/CreateER.pl "Please \\n ignore \\n my friend");
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Memory and cursory googling point toward backslash being an escape character in Java, as well as Perl... Thus, your perl program is getting those as literal line breaks.

Essentially, it's being called as:

c:/perl.exe C:/CreateER.pl "Please
 ignore 
 my friend"
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Update: I tested my theory in Eclipse. A: I was correct. B: You totally owe me a coke for making me have to deal with eclipse ;-)