I have some problem with spi

I use BeagleBone Black to write eprom by using. after it finish writing 
EPROM and the EPROM is read by other controller there is no problem

but after I reboot controller (BBB still operate) it can not read data from 
EPROM after i checked with scope 

I saw that some SPI pin act like a ground that make other controller cannot 
get the data because they always connected together

right now my solution is just setting the pin mode back to gpio 

so is this a normal state pin of SPI?
is there any solution without swapping pin mode?

I'm using kernel 3.8.13-xenomai-r78 with debian version 7.8 and it occured 
to me too when i was using the newest image debian version 9.4 

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