threading - spindle encoder synchonization issues

Hi, I'm trying to get consistent threading working on my lathe which is a Taig lathe that I converted to CNC and is running Linuxcnc.  For a while I was trying to cut threads with just one encoder output pulse per revolution.  This seemed to work okay for coarse threads but the carriage was visibly jerky due to insufficient feedback rates. 

So now I have a 60 pulse per revolution encoder, in addition to the single pulse index.  This is a home-built encoder made by printing out 60 stripes around a circle on a transparency which is adhered to a transparent piece of plastic.  This disc runs through an optical interrupter switch. 

Now the carriage moves much more smoothly and seems to cut decent threads but not consistently.  During a threading operation, things will be going fine and then I'll get a very ragged cut that seems to be removing a lot more material than previous cuts.  Sometimes it's so bad that the tool will get clogged behind the chip and stall the spindle (these tests were mostly on aluminum, 20 tpi, 1/2" to 1" diameters). 
I'm wondering if the spindle synchronization is not working perfectly, so that occasionally the tool enters the work slightly out of phase with previous cuts, resulting in a much larger depth of cut. 

Does anyone know of any good ways to diagnose this issue?  I've done some pulse counting with a logic analyzer to verify that I'm getting the right number of pulses per revolution.  I also verified that the cross feed is advancing the correct amount each pass.  But it seems tricky to measure the precise phase of the spindle at the point when the tool enters the work. 

It could be a mechanical issue, like my tool isn't sharp enough, or maybe the tool gets deflected and ends up taking a heavy cut occasionally.  But the resulting threads look a little strange to me: not quite v shaped trenches.  More like a "u", indicating that the tool wasn't quite overlapping each pass. 

Carson

Things to check; Make sure that your encoder pulse and index signals are clean and without noise that could cause bad results. Make sure there is no possibility of a lost steps in any of the axis motion. If the encoder is software counted, make sure that you are operating well away from it's counting limits.

Good evening, as here:

Is there any value for having a spindle encoder if the spindle is simply an AC motor with a VFD?
I see the value if it is a servo drive. If I understand correctly, threading operations simply use an index pulse.

Its actually the opposite, a servo motor can maintain a precise speed but a VFD cannot...

If you only have an index, accurate threading is relying on perfect speed control for a
complete spindle rotation, since the control must guess the spindle angular  position between
index pulses. Having an encoder allows the control to "gear" X motion to spindle rotation
so even without precise spindle speed control, accurate threads can be cut.

yes, more accuracy