My threads were working fine and I was only updating templates when I got the following message:
Error including libraries: (Maybe you didn't strip carriage returns after a network transfer?)

What does "strip carriage returns after a network" transfer mean? I use Cute FTP, can I do this? This is strange as it was working fine and then it doesn't work. Thanks for any help

To answer my own question,

I figured out that I had to reconnect FTP, which put my transfer status in automatic/binary mode. I uploaded a file in binary mode which caused this problem.

Thanks.