Hi,
It sounds like you are projecting your input layers only for display, but the underlying data is still in WGS 1984.
You need to run the Project tool (Data Management -> Projections and Transformations -> Feature -> Project) on each of your data layers, setting the Output Coordinate System to 102443 (which is TWD_1997_TM_Taiwan).
Then, you can run Generate Near Table on the resulting layers. The units used should be metres.
Regards,
Simon