In my case, the patch was generated perfectly fine by IDEA, however, I edited the patch and saved it which changed CRLF to LF and then the patch stopped working. Curiously, converting it back to CRLF did not work. I noticed in VI editor, that even after setting to DOS format, the '^M' were not added to the end of lines. This forced me to only make changes in VI, so that the EOLs were preserved.
This may apply to you, if you make changes in a non-Windows environment to a patch covering changes between two versions both coming from Windows environment. You want to be careful how you edit such files.
BTW ignore-whitespace
did not help.