Juan,

It takes extreme skill to make code work where events in one interrupt depend on events in another. I try to avoid it as often as I can ("takes extreme skill" = likely bugs).

One thing you can never expect to work is one thread waiting for another to do something.

I have had a brief look at your code and suggest the following change:
Interrupt a set a flag
interrupt b set a flag
Main does something based on the flags.

That is a safe and sane way to accomplish thread interaction.

Erik