Which viewport percentage spinner are you talking about? The PFlow one, or the PRT Loader one? You should probably turn the PRT Loader’s viewport display off completely since PFlow will be giving you a more accurate display of the particles.
In order to correctly load a percentage of particles in PFlow, you will need to have a valid ID channel, since it uses a hash of the ID value to determine which particles to load.
The Viewport settings of the PRT Loader should not affect anything when using the PRT Loader Birth, if they do its a bug. On the other hand, the Render settings will affect the particles seen by the PRT Loader Birth. In general, it is not a good idea to use the PRT Loader’s Load Percentage when it is sourcing particles for a PRT Loader Birth. If you do choose to do this, you will need to set the Render Load Mode to “Every Nth By ID” so that PFlow sees particles with consistent IDs.