I agree with David that the first issue related to time machine warning should be fixed by running Matlab using sudo as he explained. As such this should not affect the rest of the processing and you can safely ignore that warning.
Regarding the second issue related to the error during svreg processing, I think the surfaces are not probably extracted correctly. Before running SVReg, did the surfaces look like the ones shown in the screenshot below (right bottom windows)?
http://brainsuite.org/wp-content/uploads/2015/01/hemisplitpic.png
If you can post or email me a screenshot that will help in addressing this.