Unfortunately, I'm just now experiencing the same thing. It started happening immediately after I update to Chrome 25. It's not clear yet that Chrome 25 is the issue. Here is what I did;
1) I was in Chrome 23, happily using code server for compiling and source maps and chrome dev tools for debuggging.
2) I wanted to try the new speech features in Chrome 25, so installed the beta, the restarted chrome (while eclipse and code server were running).
3) I opened up the html file again. I made some changed to my source and compiled it in chrome using the code server bookmark. It compiled correctly, but only javascript source was available. The compiler output shows the source maps are enabled. I checked the chrome dev tools setting and they indicate source maps are still enabled in chrome.
4) I then did a bunch of stuff in various combinations,refreshing the page, clearing the cache, restarting chrome, restarting code server, doing full GWT compile then starting code servers, etc. Still no source maps.
So, I'm not sure if it was the upgrading of the browser, or restarting the browser while code server was running. I'll continue to work on this and let you know what I find. If you figure this out, please reply and let me know what you found. Thanks much.
Ed