That's a perfectly legitimate question, someone's paying attention
There are 2 things that caused an increase:
1) a new library is used and bundled with muCommander: JNA (Java Native Access). It makes it possible to invoke native methods without having to mess with JNI. It is only being used under Windows, for interaction with the Recycle Bin amongst other things.
2) Code obfuscation (using Proguard) was disabled because of some weird side effects with JNA. But obfuscation would have been disabled anyway when the Plugin API got released.
Answering this question made me realize that I can save some space by trimming parts of the JNA library. The next nightly build should be almost 300KB smaller than the current one.