Beagle xM IRQ and faster-than-filesystem bitwise I/O

I have a Beagle Board xM rev C, which has been working great driving Dynamixel servos over serial/USB.  However, when I try to drive hobby (PWM based) motor controller it works really erratically.  The usleep(1000) call, for example, can sleep anywhere from 1000 to 1500uS, making servos jiggle and move un-smoothly.  Perhaps part of the problem is that to drive the bits (I/O lines) which connect to the motor controller, I am using what looks like a lot of file opens and closes and fprintf calls.  This could be causing erratic timing too.  Also I am not using an ISR or IRQ structure but rather a simple main program which loops and calls uSleep().  Is there a better way such as to use timers and/or interrupts?  Is there any way to have the tightly-timed calls go some other rout than the file-system?  I programmed QNX a decade ago so am familiar somewhat with that approach.  I also am working on getting WiFi (through a USB dongle) working so I can SSH to the board.  Thank you!