When repeating system optimization on OS X 10.11, the report shows many “Unable to unlink” error messages at the end: If you are using the feature Maintenance > Repeat System Optimization while System Integrity Protection is active, the main part of the procedure will be executed correctly, but at the end, OS X might record many warning messages of the pattern update_dyld_shared_cache[…]: Unable to unlink //var/db/spindump/OLDDSC … 1 Operation not permitted.
Workaround: This is a known design flaw of OS X El Capitan. Apple has not made this part of the operating system compatible with System Integrity Protection yet. You can safely ignore these messages.
The feature to reset the App privacy database may not work as expected for specific domains: If you select some of the items in the App Privacy table on the Privacy pane and press the Reset button, there may not always be a noticeable effect on the privacy settings. Depending on what domain of personal data you had chosen, OS X Yosemite may just ignore the command, reporting that the reset operation has been performed successfully.
Workaround: This is a known defect of OS X. Apple may or may not fix this problem in future versions of the operating system. If the automatic reset operation appears to fail, try to delete the individual items manually in the Privacy table of the Security & Privacy pane of System Preferences.
When OS X asks for permission to let TinkerTool System execute a privileged operation, the password panel has no keyboard focus: Depending on the authorization policies set forth in your operating system, OS X automatically opens a panel to enter name and password of an administrator each time TinkerTool System likes to perform an operation which requires more than the usual rights of your user account. In this panel, the password entry field is not pre-activated, i.e. it does not receive input from the keyboard immediately. You have to click onto the panel or its fields first before you can type your input.
Workaround: This is a known issue of current versions of OS X. Applications which use multi-tier privilege separation (like TinkerTool System 4) to fulfill Apple’s highest standards for system security cannot force OS X to display an authentication panel that becomes active immediately. In addition, the lock icon in the panel also won’t show an additional badge icon for TinkerTool System. We have informed Apple about this issue and hope they will fix it in future versions of OS X.
TinkerTool System may automatically quit if it is forced to open manipulated third-party applications: The application can quit immediately without displaying an error message first, when you are using a feature that analyzes the contents of a third-party application which contains untrusted, manipulated code. The line Exception Type: EXC_CRASH (Code Signature Invalid) can be found in the associated crash log.
Workaround: Although this looks like a crash and the operating system is creating a crash log, this is not an actual crash but the correct and intended behavior of a security feature established by TinkerTool System and OS X. The application actively tries to avoid that any bad program code can reach its memory area. If you are using functions which cause the application to read code parts of other programs (e.g. selecting one of the “thinning” features) and OS X “knows” already that this other code cannot be trusted, high-security applications like the Finder and TinkerTool System will immediately shut down as a security measure, preventing that the bad code could contaminate them. The best solution to avoid this problem is to delete the bad third-party software. If you don’t like to do this, you must avoid that the bad software can run in the same OS session before TinkerTool System should open it. (Restart the computer, preventing that the bad software can run, and only then let TinkerTool System work on the bad software if necessary.)