benbot wrote:Why are there so many different ways to pronounce the same kanji in the kunyomi readings?
Because the Japanese adapted written Chinese to write their language, and as a consequence things only fit so well. The past 1,600 years have only served to muddle things, and while the simplifications following WWII helped matters a bit, I think everyone can agree that it's still a ridiculously complicated writing system.
Do they mean different things?
Yes. While the meanings are often related, sometimes they aren't.
Which one shall i learn?
Whichever one is the most useful to you at the time. Sometimes characters will only have one or two readings, so that simplifies matters. Others are more complicated, containing quirks and exceptions that take some time to get accustomed to.