Most sea water electric toilets need an electric solenoid valve in the vented loop...wired to the flush button that closes and opens it. Whether you have one, or even need one, for your remote intake pump, I wonder if it's vented loop that's preventing your washdown pump from priming. If so, the solution may be a solenoid valve wired so that either the toilet or the washdown pump can activate it.

That's just a WAG...if it's not the answer, give Vic at Raritan call...he's great at solving li'l problems like this. 800-352-5630 x 6.