Ok, so I had success in fixing my problem thanks to Nick's suggestions. I re-initialized all my factors and FactorLib was able to recognize all of them. So these were the steps I did:
1. Re-initialize pedal according to the manual
2. Plug USB into pedal once pedal was re-initialized
3. Open up FactorLib on my pc
4. Plug other end of USB cable into my pc
5. Go to midi configuration, selecting the appropriate factor pedal and hittinh "ok"
6. Go to "File" and select "Open From Midi" (or click the button on the toolbar
7. Watch the pedal do its thing.
Again, thank you Nick for your suggestions, I can now load presets on my pedals 
