They are actively being read on boot up and any loads on them, your other devices, will affect the booting mode of the processor.
Check the SRM https://github.com/CircuitCo/BeagleBone-Black/blob/master/BBB_SRM.pdf?raw=true , check the data sheet http://www.ti.com/product/AM3358 and search this mailing list. They will all tell you the same thing.
You can also check: http://www.elinux.org/Beagleboard:BeagleBoneBlack#Expansion_Header_Pin_Usage
Do not apply any load to those pins until after the SYS_RESET line goes high. Another thing you can try is to apply lower resistance pullups and pulldowns that match the ones on the board, except with a lower value. That will affect the video, but as you want to use them for outputs, the lower values should be OK.
Gerald
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