As it was a fixing issue the presoaking lack should not be a contributing factor in the brown stains.
Also it should be noted that in the case of FP4+ Ilford recommends not using presoaking (pre-rinse): "A pre-rinse is not recommended as it can lead to uneven processing." http://largeformatfilm.com/FP4-plus.pdf , page 3.
This is because Ilford says that presoaking removes surfactants from emulsion that they include in it to ensure an even development.
Berger product may have other processing recommendations...
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