I have encountered a drain like you described, and it stems from the subscribe code selecting all the recent posts and then using the top x (the subscribe max e-mails) rather than selecting just x posts. I've made this and several other optimizations in the subscription handling for 1.1.7 to fix this problem - try downloading the attached files (admin/GForum/Subscribe.pm and admin/cron/subscribe.pl) and see if it still drains system resources. Note that you will probably need to edit the "use lib" and GForum::init() lines in subscribe.pl if you download this.
subscribe.pl has a new option: -f. With this update (and thus 1.1.7) you can change your cron job to run:
/path/to/admin/cron/subscribe.pl -s -d -f "/path/to/admin/cron/subscribe.log"
It will enable debug mode and log the debugging into the file specified. This can help diagnose exactly where any problem and/or slowdown in the subscribing is happening. Don't leave the -d and -f options on permanently - they'll slowly fill up your drive and slow the subscription down a little bit.
Jason Rhinelander
Gossamer Threads jason@gossamer-threads.com