7I43 or 5I20

Hi!
I need to make stable and precession lathe. The detail tolerance is 0.03 mm and the moving of X and Z are at the same time (cone processing).
In the first lathe (build one year ago) I used 5i20. All works fine. In the recent lathe (build month ago) I used 7I47.
All the hardware and software is the same (identical).
But the stable of 5i20 lathe is more then 7i43 (statistic is sigma = 0.01 mm for 5i20 and sigma = 0.03 mm for 7i43. Measurement was done in 100 pcs.).
Loading software - SVST2_4_7I47.
My question:
Is PCI bus (5i20) is better then LPT (7i47)?
The servo thread is 1000000 ns = 1000 mks = 1mS or 1kHz.
The 5i20 clock is 33 Mhz, but 7i43 clock is 50 Mhz. Looks like the 7i43 is more faster then 5i20.
Is it right or not?
Are these two boards identical for my case or I need to use PCI for higher precession?
Please write you oppinion!

Are you using normal hardware stepgens or are you using encoder feedback?
How much jitter does your system have?
I would not expect much difference with the 7I43 and the 5I20 but tuning
might be somewhat different since the 7I43 host interface is quite a bit slower
than the PCI card interface (host communication with the 7I43 is about 6 to
12 times slower than a PCI card like the 5I20/22/23/25)

I use 2 stepgens (X and Z) and 3 encoders (X, Z, Spindle).
All hal configuration is similar in both lathe.
I also use all gpio. All 48 contacts (with stepgen, encoder and PWM) are connected to input/output devices and buttons.

Since you are using stepgens with PID feedback it may simply be that tuning is slightly different between the 7I43 and 5I20
I would expect some small difference in optimum tuning because of the differing I/O delays between the cards

The working velocity is very low.
The amount velocity is 25mm/min. This velocity divided per axis:
X = 0.047 mm/sec
Z = 0.470 mm/sec
I use SCALE factor = 1000, so one encoder tick = 0.001 mm.
But 5i20 working more stable then 7i43.

Probably just tuning