strtotime uses the unix timestamp, not they mysql timestamp. The primary reason is that unix timestamps are a 100 times easier to use, compare, format, you name it. If you ever need to do something with a date, you will probably end up converting it to a unix timestamp first. Consequently unix timestamps are used much more frequently. The only advantage to the mysql timestamp is that it's human readable and doesn't have a date range limit. You are better of storing the times as unix timestamps, and just using date() when you need to format them.
Run a few of your numbers through strtotime, and then use date() to see if it was processed right. If it doesn't come out right, then try a str_replace or preg_replace to format your text to look a little more normal.
