Update:
we tried with the ICS branch supplied kernel and .ko modules -from the configuration the worked perfectly- combined with the JB root filesystem (we simply copied kernel directory to this branch and after build overwrote the kernel modules) and we still get the sdio error.
Th conclusion is that on kernel level what worked on ICS does not work on JB so my only idea here is that the problem is in the .bin file or the .ini files somewhere around the /system/etc/firmware/ section.
Guys? What do you think?
best regards,
sodjas