Strange SPI behavior with a Microchip 25LC01
One thing I notice is that in the first trace, you start with the clock high.  Note that the datasheet shows the clock being low at the time chip select goes low.

It's also strange that MISO goes thru three states in the first diagram.  It should be floating at first, so should be driven by only whatever pullup or pulldown you have on the line.  The intermediate level after 8 clocks is strange because it's not solidly high or low.  But then MISO goes fully low after chip select is de-asserted.

This almost seems like there is something else driving MISO than just the selected device and a weak pullup or pulldown somewhere.  Maybe some other device on the bus is accidentally tied to the same chip select, or is always selected for some reason.

Sometimes it's easier to debug strange SPI problems by driving the bus strictly from firmware.  That way you can guarantee to be changing only one output at a time, with some minimum time between changes and when inputs are read.  Once you get the correct response from the device, you can go back to the SPI hardware and compare how its different.