Interesting that you mentioned that. I have noticed one pattern on 3 AA award reservations involving IB business class with disappearing seat assignments... maybe it's just a coincidence and I am reading too much into it, but at least in those 3 examples, the seats stayed on odd segments and dissapeared in even segments.

For example, one was
1 IB Europe-MAD (seat assigned ok)
2 IB MAD-South America
3 LP
...

another one
1 AA
2 BA
3 IB Europe-MAD (seat assigned ok)
4 IB MAD-South America
5 LP
...

another one
1 USA-MAD (seat assigned ok)
2 MAD-Europe
3 AA
...

At first I thought that they could only assign seats on the short segments, but not on the transatlantic ones, but the last reservation shot down that theory. Then I thought about the even/odd segments. It makes absolutely no sense to me, but maybe there is a pattern?