@geep -
Yup, the 2.3 problem was due to a null byte in the UART buffer triggering the new binary access mode accidentally. I increased the number of 0's required to enter binary mode and it seems to have fixed the problem.
What settings are you using with the serial IO? (speed, databits&polarity, stop bits, RX polarity, and output type)
What is the source and voltage of the serial data?
Do you have anything else enabled like pullups, voltage regulators, etc?
Can you jumper the MISO and MOSI pins and test that data goes correctly between the TX and RX pins of the Bus Pirate itself?
I tested on the same Bus Pirate, and between two different version, without any problems. So it could be some settings that are still universally messed up. The output looks fine on a logic analyizer, so the TX side configuration should be working now. I don't have any other serial IO sources, but I'll try to pull something together.