When using the debugger in VAJ3 sometimes certain variables are not visible. Why?

This is a symptom of an optimization the VAJ compiler is doing. If you define a variable which is not referenced, the compiler will optimize it away (remove it) as if you never included it. Even assigning a value to the variable is not enough to keep it around. For example:

int i;
...
i = 1;
...
the rest of the method, with no reference to i
...

During run-time in the debugger, holding the mouse over i will not show anything because i is not used in the program.

Also, if you edit any code in the debugger, it will not display any variables until you have saved the changes.