You need to pass "-:c" flag to csi. (I guessed it from emacs plugin)
So, you have to edit a bit SublimeREPL/config/Scheme/Main.sublime-menu
. In my case is in the path (I'm in osx):
~/Library/Application\ Support/Sublime\ Text\ 2/Packages/SublimeREPL/config/Scheme/Main.sublime-menu
The file looks like Main.sublime-menu.
Now you have to edit how the shell is open for scheme. So, go to the line 24 (for osx) and change the line:
"osx": ["scheme"],
by:
"osx": ["csi", "-:c"],
If you are in linux or windows, the fix is the same but, you have to edit line 23 or 25.
If you don't use "-:c" flag you will experiment the problem that you are talking about