PRT Volume objects don’t have an ID channel to save unless you create one. The simplest approach is to create a KCM that writes the Index into the ID channel (which is what the PFlow op is doing, but warning you about). The reason this is not automatic is that the Index is not a valid ID when using anything other than a single frame.
You can use the Krakatoa Particle Data Viewer to determine what exactly is going on in your particles. Its a spreadsheet like window that shows all the channels and their values for your particles. Just select the PRT Loader and select “Launch the Particle Data Viewer Utility …” from the Krakatoa menu bar.