The UNIX/Linux Discovery Wizard in SCOM 2012 R2 can fail with the error message :
"Data at the root level is invalid. Line 2, position 1" .
This problem can of course have different reasons but in our case we figured out that the problem is caused because of a problem in the Linux Resource Pool. We basically created a new Resource Pool and tried to discover the Linux computer again and we were able to discover it successfully.
Good luck !