Interesting. In your question as it currently stands, both links go the the same URL (your escape failed).
However, in the editing view the the first link as shown in the preview is properly escaped.
So, the issue here seems to be "why is the preview parsing links differently from the actual post?". More specifically, using a backslash to escape the trailing parenthesis works in the preview (!) but not in the actual post.
That aside, you can avoid having to manually escape the chars if use the appropriate markdown for linking. See Would it be possible to fix links containing parentheses in comments?
Also note the Bare URLs section in the editing help page which states that you should enclose the bare URLs with angle brackets if they contain unusual chars, or use the proper markdown syntax for linking.
Example: Raw link enclosed in angle brackets - http://developer.android.com/reference/android/content/Intent.html#addCategory(java.lang.String)