harald, i don't see a bug here.
i tried it with 5.9.3 on windows and linux, and in both cases
i get a single question, to which i can answer either p or n
to get two different (and apparently correct) results.
> (%i2) integrate(1/(a*x^2+b), x);
> Is a b positive or negative?
>
> Is a b positive or negative?
>
> Is a b positive or negative?
do you mean to say that the message "Is a b positive or negative?"
is printed repeatedly without any interaction from you?
if so, that makes me think the stream handling stuff is
messed up, although i really don't know. perhaps you
can give us a little more detail.
best,
robert dodier