I know you mentioned that both are the same size master cylinders (3/4"), however it sounds like you don't have enough fluid displaced by the master cylinder to fill up the throw out bearing enough to disengage the clutch.
I know I have addressed this issue numerous times on this forum. Simply put, whether you are dealing with brake calipers or throw out bearings, the master cylinder when fully depressed must displace enough fluid to move the caliper piston or bearing in the throw out bearing, the distance you want.
My thoughts are, in your first set up, the throw out bearing may have not had to travel far to disengage the clutch AND it was almost maxed out. Now it has to travel a little farther and you have a situation.
Hope this helps.
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