The only way to ensure that a soundtrack will not be blocked is to avoid using audio that belongs to someone else, and is protected by copyright. The only soundtracks that get flagged are those where the copyright owner has said they didn't want their tracks used.
You should realize that this actually prevents a whole lot more trouble, and is a good thing. If a copyright owner didn't want their tracks used, and YouTube didn't offer this option, the other choice would be to have lawyers contact the people that posted the video with a cease and desist notice. Most people would prefer the audio be muted than have legal notices being sent.
This site lists places you can find audio tracks that are licensed under Creative Commons, which you can use in videos without having to worry about it. It may be a better idea to get audio tracks that are under a license such as this instead of other copyrighted works. http://creativecommons.org/legalmusicforvideos
It has been pointed out in the comments that this answer assumes there are no false-positives in YouTube's ContentID system. The original question asked if there was any way to find out if a track would be blocked by YouTube before uploading a video. Whether a false-positive, or a legitimate copyright claim, the end result is still the audio being muted on the video, which is what the OP was asking about.
It was also mentioned that YouTube does allow copyrighted works to be used where they have an agreement with the label. This is also true, and in this case they will show ads on your video which the labels make money from. However, this is still irrelevant to the question that was actually asked. You have no idea until a video is uploaded if the audio will be allowed or not as there are no tools to allow you to figure out what tracks they have an agreement for, and which they don't.
So the answer to the question that was posted is still the same. There is no way to know ahead of time if a copyrighted track will be allowed, and by using copyrighted works you will always run the risk of the audio being muted when you upload the video.
As a side note, for the videos that do use copyrighted works, and are allowed as a result of an agreement with the labels, what happens when the labels and YouTube cannot agree the next time they negotiate on how much money the labels should get? These things happen, especially at a time where labels are increasingly becoming less important, and they are looking to bring in as much money as they can. As soon as the agreement falls apart all of the audio licensed by that label would be muted as well. So even if you get lucky and the track you use is allowed right now, that's not to say it would be allowed in the future, and it could be muted at any time. The ONLY way to ensure that the audio will not be muted in your videos is to use music that has been licensed for use, like Creative Commons for example, or use your own original works. Other than that there really is no way at all to ensure your videos will not be muted now, or in the future.