Did you try your process with different nice-values (i.e. using "nice --adjustment=-20 perl <yourscript>" as root) ? If you change the priority of the process significantly and the number of occurrences of the spikes changes, the problem is that other processes sometimes get in your way. If it doesn't change it might be perl itself as someone else here already suggested.

Note that there is also a realtime priority setting on linux for processes. RT is a higher priority than the highest normal priority setting (which is -20). You can see it with top, or with "ps -eo pid,tid,rtprio,ni,pri". Look at the third column which is '-' for most processes but on my system two processes have a 99 in that column.