Can you elaborate on die? Do you mean, your GUI window disappears, or does the GUI freeze ... ?

You could check:

• the return value $call: was a signal caught?
• the string given to system(): does it contain characters which are interpreted by the shell - maybe in the 'C'-case only? Alternatively, try system with a list argument.
• for any output your chain of calls send to STDOUT and STDERR
• experimentally, if the problem is in your GUI by running e.g. system("sleep 2000") instead of call_B.pl
• memory consumption again

Because of ...is submitted and returned, even C is still running..., maybe an unescaped & sneaked into the system call? That could also explain the uninitialised $res, because the result is not yet ready for long running tasks when the GUI checks for the result-files existence. For short running tasks, some (maybe not all) results are processed and the result file is already opened/created, giving the impression the GUI work fine for small tasks. Well, just some speculations...