The time taken for the Purification Chamber varies, depending on the shadow you have in it and the flow tempo. (Or whatever the tempo thing is called)
If your tempo is at maximum, the process of purification will be greatly increased, where as having a weak tempo would slow the purification process.
Also, the pokemon you're purifying plays a role in the process. If it's something like a Ralts, it usually doesn't take too long to purify, whereas an Articuno or another legendary would take a lot longer.
I suggest you read up on the Purification Chamber, the main site should have useful information.
EDIT: Go here :
http://www.serebii.net/xd/hall.shtml for information on the Purification Chamber and how it works.
~Aquarelle