If the code you are copying is from the Regular Pronto section (CCF) then yes PENG will change the code. The code is converted from the way a CCF reads it to the way a PCF reads it.
This is the code for Video 4 on a Sony TV the way that PENG saves it... 0000 0067 0000 000D 0060 0019 0030 0018 0030 0018 0030 0018 0018 0018 0018 0019 0018 0018 0030 0018 0030 0018 0018 0018 0018 0019 0018 0018 0018 03F5 This is the same code from a CCF 0000 0067 0000 000d 0060 0019 0030 0018 0030 0018 0030 0018 0018 0018 0018 0019 0018 0018 0030 0018 0030 0018 0018 0018 0018 0019 0018 0018 0018 03f4