Emulation is not inherently glitchy, once everything is set correctly.

The biggest thing you have to do is disable checksum, by changing the MASK ID in the bin to AA. This goes for all OBD1 GM ECMs.

Sometimes the APU1 needs other settings in the XDF and/or the ADX changed to be able to emulate and catalog at the same time, but $0D is not one of the masks that should need that.

Make sure you have the proper hardware selected in Preferences > dataloging.

Make sure you have the switches on the APU1 set correctly for emulation.

I suspect most of your issues are coming from not disabling the Checksum though. Start with that.

Just for refer6i own and use both the Ostrich 2.0 and the APU1.