A bit of Super Searching found ...

Timeout with SIG{ALRM} not working as expected

Random Walk's note at the bottom may hold the key.

Re^5: Splitting one large timeout into few smaller ones..

Roy Johnson has some code you can steal/adapt.

Timeout on system command

Looks like a similar problem ... and even has links to more nodes on the problem

system() with timeout

Again, similar problem - with some sage advice

Hope these help. For the record, I searched on "fork kill alarm".