I did some experiments. It turns out that PB4 can not be used as a digital input while the SPI module is enabled (PINB bit 4 is always 0). We already knew that using PB4 as a digital input could cause the SPI module to fail (that's why the SVP user's guide says that we recommend making PB4 an output), but we didn't know that SPI causes digital input to fail. If you really want to use PB4 as an input, you can temporarily disable the SPI module (by clearing the SPE bit in SPCR).
So jlake, if you want to get all 8 of your QTR sensors working right now, I suggest adding code around your QTR-reading code like this:
unsigned char saved_spcr = SPCR; // Save the state of the SPI module
SPCR &= ~(1<<SPE); // Disable SPI module so PB4 can be used as input
qtr_read(values, QTR_EMITTERS_ON); // change this to whatever type of QTR reading you want to do
set_digital_output(IO_B4, LOW); // Make PB4 an output so it doesn't interfere with SPI.
SPCR = saved_spcr; // Restore the state of the SPI module.
This code worked for me, allowing me to read analog channel A from the auxiliary processor via SPI and also read a QTR-RC sensor on PB4 in the same program. This code also works if you drive PB4 high instead of low, but that would cause increased power consumption.
Also, later today we should have a new version of the Pololu AVR Library out that allows you to use pins A0-A7 for your sensors, so you won't have to deal with the quirks of PB4. When we release it, we'll make an announcement in the announcements forum.