problem with 2.6.1 and Power PC
 

I was happy to see that SuperDuper was upgraded for Snow Leopard, and it has worked fine on my Intel MacBook Pro, but it failed to work on my G5. It hung on repairing permissions for 12 hours and did the same after several restarts. So I downgraded to 2.5 from a previous backup (by the way, how do find earlier versions online when you need them?) and it worked fine. Are there any problems I should be aware of using 2.5 with OS X 10.5.8?

Regarding 2.5 and 10.5.8, I have done that since 10.5.8 came out, and there are no problems peculiar to that combo. Works in normal SD fashion.

Well, "repair permissions" is just done with Disk Utility (we ask it to do it, and it returns to us), so perhaps your system was in a weird state? I'd go back to 2.6.1, and remember to recreate any scheduled copies.