We removed the Philips MF RC531 chip and started checking the signals of the ATMEL chip (during external access) at Oscilloscope level. Then we found something different.......During the readregister, however the chip select is proper, but there is no RD pulse within the chip select. A very meagre spike alone is seen.
In the hardware something (that was removed?) has held !RD at a hard high. This will pop the port pin.

Erik