My 3d printer has been working fine for over a year.  The cpu latency went south
and I added a MESA 5i25 board.

The motion control x,y,z,a all work perfectly. I have cut that part out to
work only on the encoder,pid, and pwm.

My problem is with the encoder, pid, pwmgenerator.
This part of the code worked ok on the original parallel port.
I am interfacing through a geco 540 which takes a digital signal from a 555 timer IC
with r2 a 100k thermistor to set frequency.

The current readings are:
The frequency encoder 1 velocity  is 1.6  @ 17 degrees c
The frequency encoder 1 velocity  is 4.6  @ 70 degrees c
The frequency encoder 1 velocity  is 4.6  @ 100 degrees c
I do not get pwm dutycycle or pid output. Also no pwm to output pins.
The output pins are connected corectly as I can send input directly to output pins 
and observe on halscope.