Please, can you keep the mailing list in the CC, so others may benefit from our discussion and answer at the bottom of the email (bottom posting ) to make it easier to follow the message thread.
Can you give a short example of "ga_stalagmite.m" up to line 25, which is not part of the ga package and triggers the bug? By just looking at the respective code lines of the error message, I cannot give any useful hints. Somehow non-integer indices are created in a situation like the following short example:
>> A = [1 2 3 4 5];
error: A(0.333333): subscripts must be either integers 1 to (2^63)-1 or logicals
This should be avoided in your code.