I'm sorry to tell you this, but again, IP is always a specific amount above ambient pressure. That's the way all regulators function; if not, they would not work for diving at various depths. The pressure differential between ambient and IP is the same regardless if you're at sea level, on the top of Mt Everest, or at 200ft of depth.
Plus, what you're saying with "the pressure differential not being sufficient to keep the valves closed" makes no sense, here's why. For the 2nd stage valves, IP is trying to open the valves, not close them. Less pressure differential between ambient and IP (or, for all intents and purposes, lower IP) would result in less force opening the 2nd stages, i.e higher cracking pressure, not lower. It would make a slight free flow less likely, not more.
For the first stage valve, IP is by definition the pressure required to close the valve. If there's a leak at that valve, it means IP is creeping up. If your free flow was caused by IP creep, which is a possibility given that the balanced 2nds did not leak, then you need to start by measuring the IP and making sure it locks up quickly and within the given spec, which for SP 1st stages is between 125 and 150 PSI. I like to set my balance piston SP 1st stages on the low side, around 130.
What I had been wondering about was if there was something that would prevent the first stage from automatically compensating, i.e lowering, the IP at altitude. That would result in a higher-than-normal IP, or a larger pressure differential from ambient. That could cause a leak. But I can't think of anything that would cause that. Maybe some sort of problem with something like the sherwood dry bleed system, but that's a stretch.
So I suspect your leaks had nothing to do with altitude; much more likely they were related to the recent service. Slight freeflows, especially in unbalanced 2nds are not uncommon after service.