Hey NK,
I had a very similar problem but only with the hand pump but depending on how it is plumbed in it could be also affect the pump system. I found that the pipe from the hand pump was plumbed in between the 3 way switch and the rear tank so when rear tank was empty and wanted to draw from the front tank, all it would do is suck air from the rear tank and not suck water from the front. I assumed that the hand pump would be plumbed onto the switched side of the 3 way switch so that whichever tank I wanted to draw from I could select. But after investigation under the van I found that was not the case. The way I fixed this was to put a stopcock just before the rear tank. So when I want to use the front tank I close the stopcock so I cannot draw air from that tank and it primes from the front tank. The way I got around this on the road when I first discovered it was to disconnect 10mm pipe from rear tank. Put a plastic bag over the end and use the hose clamp to tighten it over the pipe to block it. Just remember to put it back on before driving off do u don't fill the tank with dust.