This posting is older than 6 months and can contain outdated information.
What you describe is definately not a Remote Buddy problem:
1) Remote Buddy only attaches to one device - being your Keyspan IR 
Receiver. The hub, to which all other devices are connected, is up two 
to three levels in the driver tree, including a kernel/userspace 
barrier that Remote Buddy can't cross (no userspace clients are 
available for IOUSBHub objects AFAIK - and even if they were, Remote 
Buddy does not look for or use them).
2) Remote Buddy generally has no interest in hubs and leaves them 
completely alone.
3) Built-in trackpad and keyboard are internally connected through 
USB, but usually they're connected via a different, internal port / hub.
4) On a PowerMac with Keyspan IR receiver (as in your case), Remote 
Buddy's kernel extension does nothing USB related at all. As of now, 
the kernel extension only contains code relating to built-in IR 
receivers and Keyspan *RF* Remote for Front Row.
There's been a lot of coverage on a bug of the (re)new(ed) USB stack 
in Leopard that causes the exact problem you describe. Here's a 
randomly selected article:
http://www.techworld.com/opsys/news/index.cfm?newsid=10644
You may want to file a bug with Apple at
http://bugreporter.apple.com/
to inform them about the problem.
That said, here's a short update:
The (different) problem that built-in IR receivers are sometimes not 
found after a wake on Leopard is also related to changes in Leopard's 
USB stack and requires a somewhat more complex, pretty code-intensive 
workaround and a completely new design approach, which I've almost 
finished.
Best regards, 
Felix
Am 09.12.2007 um 17:01 schrieb ..:
 Oops... I found why RB wont work on my PM G4, when i have my Keyspan 
IR remote conncted to my mac with RB running and put it to sleep the 
USB port stops working, nothing will work on it. Mice, keyboard and 
USB-flash memory, i will test it on my other USB-port today.