There are several reasons why OS X may not accept start-up arguments, though sometimes the reasons can be bizarre and unexpected.
Sometimes problems happen for what turn out to be rather bizarre reasons. Recently we were contacted by MacFixIt reader "Frank" who had a long-standing problem where his Mac Pro would not accept boot arguments such as booting to Safe Mode when holding the Shift key.
Many times when boot commands are not working people suspect either the PRAM, the SMC, or an enabled firmware password is the root of the problem; however, this is not always the case. Sometimes incompatible hardware or faults in hardware can interfere with the ability to pass boot arguments to the system, though this usually is with core hardware components such as RAM, expansion cards, or hard drives.
In Frank's situation, what ended up being the problem was the third-party extender cable he was using with his Apple USB keyboard. While such a cable would usually be overlooked, in this case when he replaced it with an Apple-supplied extender cable the system began accepting boot arguments again.
Being essentially a few lengths of wire with no logic components in them, extender cables would not be expected to cause such problems, especially when the same cable works fine at transmitting keyboard input to the system once the OS is loaded. Despite this, it is possible that faults in the cabling could result in abnormally high resistance, and thereby lead to smaller signals being sent to the system. If having drivers loaded versus running off the firmware code for managing the keyboard somehow allows the key presses to be recognized better, then this could be one possible reason why a faulty cable would work properly after bootup, but not during or before it.
Be sure to check for problems with and try alternative cables if you are having troubles with various devices. Even if you do not initially suspect the cable, it cannot hurt to just swap it out as an initial troubleshooting step.
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