Hang during boot process

Weve manage to embed photon and place it to a 16MB DiskonChip 2000.
Everything works fine except we found a problem on the boot loader.
We need to have a stable system that we need to soft boot once in a
while, say for example every 5 minutes. We manage to do that but
sometimes it gets stuck on the boot process. The last thing we saw
on the pc was

Booting partition 1?1
Press Esc for .altboot…

We are testing for weeks to fix this problem, and the weird thing is
that most of the time , the boot process proceeds properly but after
some hours, we get this problem.

Can someone give us some idea how we can fix this, i think its somewhere
on the boot loader…