What PSI does your Hobbs trigger at?
The FPCM acts independently of the ECM tune for the most part, even though you're only using it as essentially a relay to trigger your 2nd pump. The FPCM is pulse-width modulated so although I am not familiar with using it in the fashion you are, I'd make sure I'm not getting variable voltage on my trigger wire - pumps will run even when they're not PWM compatible, but won't reach full flow and die early.
My second suggestion is to look at making sure you are hitting "high flow" early enough (ie lower the fuel flow limit to trigger it earlier) to make sure the FPCM isn't trying to modulate or cut out the pump based on it's confused expectation of what your flow and fuel pressure should be doing.
The FPCM acts independently of the ECM tune for the most part, even though you're only using it as essentially a relay to trigger your 2nd pump. The FPCM is pulse-width modulated so although I am not familiar with using it in the fashion you are, I'd make sure I'm not getting variable voltage on my trigger wire - pumps will run even when they're not PWM compatible, but won't reach full flow and die early.
My second suggestion is to look at making sure you are hitting "high flow" early enough (ie lower the fuel flow limit to trigger it earlier) to make sure the FPCM isn't trying to modulate or cut out the pump based on it's confused expectation of what your flow and fuel pressure should be doing.