CRVTEC Ignition Timing problems with S300

[CRVTEC0WNZJ00]

Checking timing on my engine after taking care of some wiring and some other mechanical details. Anyway, car is a 1993 Honda Civic Si with a CR/VTEC engine. The details in short are B20B4 block with JE 11:5:1 pistons and other lower end internals and a stock 2000 ITR head with bolt ons like throttle body intake manifold, header exhaust the usual. Well running Hondata S300 to tune with and the PLXM300 wideband O2 sensor. Using a 1994 Integra SiRG distributor with new cap and rotor and basically everything is new except the dizzy and some other stuff.
The story so far:

Set base ignition timing by jumping the 2 pin DLC connector with a paperclip which sets the CEL light on and supposedly disables timing advance. At an idle of about 850rpm the Hondata says we're running 22 degrees of timing however when reading the timing light we are dead on 16 degrees. At 3000rpm's the timing light reads about 32 degrees of timing and the Hondata will read 42+ degrees of ignition timing. I'm curious if anyone else has had this issue or if there is anyway to change the parameters for the ignition timing not by changing the correction values. As far as I know this can't be done. However I was assuming since this engine uses only a CMP or cam position sensor or cam angle sensor which ever you want to call it....I was thinking that the distributor shafts bearings could be worn leaving the distributor shaft wobbling slightly causing a misinterpretation at the ECU. I'm looking for any information or any common problems people have had setting ignition timing using Hondata or any similar software. Any help would be greatly appreciated. If there are arny more questions on the specifics of the build I'll be glad to share full details. This is just really throwing me off on the ignition timing it should read the same on the Hondata and the timing light.

[RMS]

are you synch'ing the timing (turning the dizzy to match the timing light#s to the ignition map?).

[jdmspecdc5]

bump. would like to know this too. and how to check base timing in smanager?