The problem was solved as in the direction Chris Haas pointed out. It does not mean other answers don't work, it just means the problem can be solved at least in one way.
Here it is, simply adding "/C "
in the code, and it should work:
Original that did not work:
string fijiCmdText = "D:\\fiji\\fiji.exe -macro D:\\fiji\\macros\\FFTBatch.ijm --headless";
System.Diagnostics.Process.Start("cmd.exe", fijiCmdText)
;
Current code that works:
string fijiCmdText = "/C D:\\fiji\\fiji.exe -macro D:\\fiji\\macros\\FFTBatch.ijm --headless";
System.Diagnostics.Process.Start("cmd.exe", fijiCmdText);
Here is the reference mentioned by Chris Haas. See EDIT3