I see the same problem with irrigation controllers in golf courses and HOAs. The landscaper always blames the GFCI outlet or breaker, but it always ends up being leakage or other faults in the irrigation controller (often a tansformer that's heading south).
I think you are handling the problem well by demonstrating to the customer that more than one GFCI trips with the same device. It narrows the problem down to the device, and involves the customer in the troubleshooting process.
Fountain pumps are becoming an off-the-shelf product that are commonly available to your average Home Depot/Lowes shopper, so competitive pricing leads fountain installers and manufacturers to supply cheaper units. We're bound to see abundant failures.
