The echo is much more likely to find the VSD than the MRI.
Hearing a quiet murmur can be very dependent on the quietness of the room that you're in. If there's a lot of background noise they can be very hard to hear. If I can hear a murmur in the ER then it's at least a level 5 out of 6. Anything less and it can't be heard. They can also vary in loudness with your position (lying vs sitting or standing), your heart rate, your respiratory rate. It's not that simple.
The seriousness of a VSD varies with the size of the hole and the symptoms that you're having.

