You can use a Xantech IR router like an RT8 (~$250, also requires a power supply, receiver, and emitters none of which are expensive) and program your universal remote so that it sends device selection codes before and after the offending commands.
Pronto .CCF files with the codes are available at remotecentral.com, for other learning remotes you might have to buy Xantech's programmer.
My theater/multi-zone control project involves netremote (A pocket PC application which can use .CCF files, and PC server which can do IR pass through) and a USB UIRT (USB IR receiver transmitter) - the hardware supports multiple IR zones although I don't know that the software does.