This thread is a bit old, but as I have just had what seems to be the same issue, I thought I would provide at least my response.
Reaper has two FX configurations, processed as either input (the IN/FX channel config. dropdown) on the and output of a track (the FX after the Mono Solo buttons). This wasn't clear to me until I went through the manual a few times and saw a YouTUbe video where someone clicked something I hadn't thought of...
FX on the output are not applied to live input, but work perfectly fine for processing WAV files, existing tracks with audio content.
A plug-in on the IN/FX will be applied instantly to the incomming audio, and will work for live streams.
The concept is a bit different, at least to me, where the output FX is for production and working with tweaking settings, while the IN/FX gets no chance for post edits.
The A-to-B format converter, for it to work on the input stream, should be loaded as an IN/FX. If, alternatively you want to apply it to an existing A-format recording, then it is fine as an output FX.
PS. I know this is on an OSX sub-forum, but I'm on Windows