Well, unless there is something else I should've done after updating, it doesn't seem to have worked here.
After updating, I let it run all day, and used "cat /proc/net/ip_conntrack | grep -c ESTABLISHED" to watch it fill up. By last night, it had filled up enough that it interrupted my net connection. Closing amule did free up about 200-300 conntrack slots. I'm not sure that it's always done that.
But there's still ~3800 ESTABLISHED amule connections this morning (out of 4096 by default on a machine with 64MB RAM ['cat /proc/sys/net/ipv4/ip_conntrack_max' to find that]). From what I've read, ESTABLISHED connections don't timeout for 5 days by default. Possibly removing the ip_conntrack module and reloading it would clear them out, but it's being used by 8 other modules, so I've just been rebooting.
Also, yesterday after a clean reboot, I opened amule and let it fill up about 200 slots or so, and then closed it and they properly went to TIME_WAIT and then closed. I'll try to see if I can figure out at what point it's not able to close all the connections anymore.
Also, I've had my max connections at 25 for awhile now. My max new connections/5 second was at 20. I also turned down the max queue size to 500 yesterday.
I'm not sure if any of this helps, but it took me awhile to figure out what was happening, so maybe this will be helpful to someone.
I'll also check back to see what newbeewan finds after running the update for awhile. I'll try rebooting too, in case something from the old version was somehow being used.