I've some problem when working on remote files (perl scripts) with Komodo IDE. There is (as far as I know) no way to change ftp transfer mode from binary to ASCII, which result in "^M" character at the end of every line. My setup is Linux server, and Windows client. Is there any way to solve this issue without nessecity of correcting saved file on Linux every time. This behaviour disqualify Komodo IDE, which was my favourite IDE until now.
The "^M" you observe has nothing to do with your file being ASCII, but line ending format (carriage return and line feed characters.)
I have not verified this, but here's a link showing how to save files in Komodo using a different line ending method. Saving files in DOS mode is not needed anymore, since most editors recognize UNIX file format nowadays.