You say the original script does nothing. I suppose this means no file is generated at all. Which would mean the line wth "open my $blast..." is never executed. Otherwise there would at least be an empty file even if the png generation failed

You can make sure of this if you just insert a line 'print "was here\n"; in that last while loop and execute the script

Now you have 3 while loops inside each other. With the same method (inserting print statements) you can find out which is the one that never gets executed. Lets assume it is really the innermost loop that never gets executed. Put the following lines just before the start of the loop:

use Data::Dumper;
print Dumper(\$hit, $hit->next_hsp);
[download]

Execute and check what you get and whether it makes sense. Compare with the data from the other script where you got one picture out (after you added a similar Dumper line). If you find the discrepancy, check where it came from. You'll find the bug in no time