A fairly unconclusive hint, but nevertheless:
I have a CA1 board (several years old) and a PE1 (from this year).
I have tried to configure the CA1 board by JTAG, and also fail, but in a different way:
Error (209015): Can't configure device. Expected JTAG ID code 0x020F70DD for device 1, but found JTAG ID code 0xFE0F70DD. Make sure the location of the target device on the circuit board matches the device's location in the device chain in the Chain Description File (.cdf).
I do not see the strange behavior on TDO.
Nevertheless, the same CA1 module can be programmed on our own base board.
Up to now, I have only used the PE1 board with an AA+ module, and that did work.
I set up the PE1 board according to the "Reference Design for Mercury+ PE1 Base Board User Manual".
Nevertheless, because it does not behave the same as in your case, I am not 100% exclude that I configured the PE1 incorrectly for the CA1.
Sorry for not checking further, but it is getting late, and am going on holiday tomorrow...
Maybe we can start a user group ;-)