Something is broken on your system then. It has nothing to do with the PocketBook SDK, because it is an existing system header file (/usr/include/bits/ioctl.h) that can't pull in the missing asm/ioctls.h file. Try building a simple native C program that includes <sys/ioctl.h> and see if that works. Maybe this is a 64/32 bit issue.
The cross-compiled versions work because the pbsdk package included asm/ioctls.h in the proper arm header directories.