Hi,
I just read this thread and discover that I was not alone... I am running last version of firmware on both TSU9400 & RFX9600, and have the same problem. I am using RS232 for volume control (Denon) and IR for Channel+/- (Freebox, French ADSL TV receiver).
==> No problem with sound level (and hoppefully, my power amp is very powerfull!)
==> I have the "bug" once or twice the month for Channel+/-, the only workaround is to reboot the RFX9600.
To my mind, the problem is link with the RFX9600 firmware: I have updated first the PE and TSU with new versions, I didn't have any problem. One month later, I have updated the RFX9600 and the problem occurs several times...

AS other people, I can upload my configuration file for Philips team (where?), but for the channel+ (for instance) this is really simple: on system/system properties page, on the Channel + button, a simple "IR Function" that point on my "Ch+" IR code. And the component is set to use IR1 on my RFX9600 extender.

Very annoying...