The RS-800 antenna is designed and tuned for the 800MHz band, so it won't perform well at all with VHF, and just does ok with the 450MHz UHF band, so that is normal. There is no perfect one-does-all antenna. The antenna supplied with your scanner makes an attempt to do that, and not very well.
It's important to know where the sites are located so you can program your scanner properly. Also, the PRO-96 was designed for one site per bank. However, if you put a null spacer frequency between the sites, you can put more than one. I used 800MHz as an example. Pick a frequency you know will not be active, and use it as a spacer. Also for your site frequencies, make sure you're only programming the control channel frequencies, not all the voice frequencies. The primary ones are in red on the RR database, and you can also program the alternate control frequencies, the ones in blue. But not the ones in black.
ie:
primary freq for site 1
alternate freq for site 1
800.0000
primary freq for site 2
alternate freq for site 2
800.0000
primary freq for site 3
alternate freq for site 3
800.0000
See if that helps.