Dahlia94,
Just load the file in that notepad++ and set the file type to unix so it converts all the line ends to unix style LF only.
The file probably has mix of unix and dos type line ends. The two are not compatible and some tools (not Modelsim) may have problems with it. Note, Modelsim is cross platform so probably ignores any line end characters (probably only checks there is one). This SYF tool probably is written and run only on unix so the programmers who wrote it didnt consider the file might have a mix of both line end styles.
I find this issue with mixed line ends occurs regularly with Xilinx's built in text editor. It shows up as a ^M at the end of lines in VIM when I edit files that were edited in Xilinx's cruddy editor.