fuel flow all over the place

[big al 08]

the rear eng fuel flow goes all over the place for 30 sec then the engine wants to quit. has happened four time from san felipe to la paz always within 45min to an hour. have gone from mmsf to kyum 40mims in between thes time with no problem. had all the pressures reset so all go to red line wot and in the green at cruise. flying between 9.5 to 13.5 depending on winds. all temps okie dokie.
it is not vapor locking. put it on low boost first time & finally settled down this last time needed to go to high boost for it settle down, if the boost are turned off after 1/2 eng quits. on final with mp at low end of the green eng quits every time. i do not believe running a long periods of time are good for the boost pumps. have an annual in ten days however need to go north and not really thrilled running the boost for four hours. any suggestions