I currently am riding a manitou 3 way SPV shock in the rear on my trek. While riding I bottomed it out and it's been making a sound that seems like its sucking air into the shock, it functions fine still. But the sound worries me of internal damage.
I used to have one of those on a Giant Team DH. The problem is probably in the SPV valve. When you bottomed, some of the air may have gotten past the seal and mixed with the oil. They always did have troubles with them and didn't make them for very long. If Manitou will rebuild it, send it back to them. But a more modern shock would be a better option if you can afford it.