1009 router, 6.41, with at least a couple ports stopped working after a reboot. Needed another reboot to get half of the ports working... Seems related to my other post about ports showing as down when they aren't. Ports still down, and are showing up.

This is a different router than my other post(s)

I had similar issues with SFP on a CCR1072.
Have you tried to disable and then enable the affected ports?
For me it worked.

which one do you have, the 7xGE or the 8xGE version?
the 8xGE version has ports 1-4 on a switch. as 6.41 has a different bridge implementation, the ports on the switch (if they were configured as master/slave) get an automatic conversion to the new style of config. if something fails, it will not be forwarding traffic and feels like it's broken.

there was another annoying issue with one of the CCR1016s i had: the led configuration was faulty - somehow port 4 as i reckon lost the appropriate led setting, so the tiny led next to the port was never lit, regardless the interface was running or link was detected.
i had to manually connect the corresponding led in '/system leds' with the appropriate interface (sfp4 in my case) to re-enable it.

other than that i don't see no valid reason other than a hw issue for your ports to stop working.
either way, you should check whether the ports are actually "there" in the "/interface" section.