The solution that worked for me is using the JD-Eclipse after applying the patch: http://java.decompiler.free.fr/?q=node/464
This is an extension of jd-eclipse which realigns the code after decompiling.
When debugging with eclipse you just need to have the jar files in the classpath and that's it!
There's no need to decompile the whole jar, realign or whatsoever... Just debug and be happy :-)
Here's how to do it:
http://gauchoacomecable.wordpress.com/2011/10/14/eclipse-debug-java-without-source-code-jd-eclipse-and-realignment/