I don't know from which version you've migrated, but I can see two possible reasons why SE should do this:
- either SE determines the encoding of your files different than you have created them, and decides to use different line endings than the files contain. You could check this in your configuration, look at Tools, Options, File Options, Load-Tab, Encoding. My installation says 'Default', which works for me, YMMV. Also, in the file extension setup, general, there's an entry for setting the encoding for certain file types.
- or the defaults for file creation (Tools, Options, File Options, Save-Tab) are set for a different file-type than you are using.
I didn't test any of these hints, though, so I don't know for sure if they reproduce the exact things you are seeing, but maybe they will help you find your culprit.
One thing you could do (but this doesn't address the problem), is to go to Tools, Options, General, Special-Characters-Tab, and replace the values for End-Of-Line 1 and two with 32 or 0x20, which is a space. The indications will be there, but invisible.