it's a very common issue not just on Magento. It's happening because of some verifications that needed to be checked before minifying.
You may want to try running JSLint on your Javascript code before you try to minimize it. JSLint might highlight some issues, which could allow you to minimize your code without error.
I recommend you try another 'minification' tool like the YUI Compressor to then upload for your CDN or just to use on your install.
Here are two articles I've found on 'A List Apart,' that may interest you, looking at the YUI Compressor.
"Better JavaScript Minification"
"JavaScript Minification Part II"