Audition not saving changes to file

The first thing here is that you can't make an edit to an MP3 file in Audition. To perform any operation at all on one, it has to be decoded to Audition's native format (wav) and when you've made whatever alterations you want, it has to be re-encoded back to being an MP3 again. This is not a lossless process - your file will be degraded. How much rather depends upon the bit rate of the file, but typically 128k files will degrade noticeably in a single pass though this process. So when you re-open the file, you are listening to a file that's been decoded, re-encoded, and then decoded again...

You haven't said how much silence you are trying to remove; it may well be that the encoder is putting it back again. Unfortunately the encoder isn't an Adobe product - it's the Fraunhofer one. There are several things you could try that might help, though. If it's just time you are trying to cut out, you'd almost certainly be better off using something like MP3DirectCut which gets around the decode/encode issue. You really can't do much more with an MP3 file directly though, so if you want to make other changes, that's probably not the route to use. The other alternative would be to re-encode using an app that opens wav files, but re-encodes using something like LAME, which almost certainly won't mess about with the timing. There is a piece of software with a name very similar to Audition that will let you do this. Normally I wouldn't recommend this software, but for this specific purpose it might be able to help you.

 If I open a MP3 I only get the option to 'save as' and I then get  the message 'are you sure you want to overwrite'.