There are two issues here — the one with Time Machine and the processing error in SVReg. They are unrelated.
For the time machine issue, this is an issue with Matlab. If you run a Matlab program once from the command line using sudo, this will fix this (see this old post on Mathworks, for example: http://www.mathworks.com/matlabcentral/answers/18762-annoying-matlab-start-up-warnings-on-mac-matlab_maci64-attempting-to-exclude-an-item-from). E.g.,
sudo /Applications/BrainSuite15c/svreg/bin/svreg.sh your_subject_file
The other issue has something to do with the surface model. Did the models look okay in the GUI?
It may be easier to address the specifics of this issue via email — do you want to email us at firstname.lastname@example.org?