When you say it converted it in 1-2 minutes, are you trying the same file again, or is this a different file?
The problem is that an MKV as a container can contain various types of video, audio and other data. Not all of these formats can be simply passed through to an MP4 container (quick) as iTunes/iOS devices can't play all the formats, in that case you need to convert (slow) which is what takes the time.