Dave, do you know for a fact that the HSE knew it stalled? Because unless somebody told them about the stalls, they probably wouldn't know about them - there is nothing in the reporting regulations RIDDOR that would require them to tell the HSE.
You are right in that the fact that a coaster stalls is not necessarily a major concern in itself. But when you design safety instrumented systems, you normally need to make assumptions about how often such safety systems will be required to operate - the so called 'demand rate'. Then, once you know the demand rate, you can work out how reliable the safety systems need to be to give a required safety integrity level. One thing the HSE will probe is what the design 'demand rate' for the ride was in terms of stalling - if it has stalled more often than anticipated, then there is a higher chance that any other safety systems may be deficient.
Way back in this thread, somebody mentioned the Swiss cheese model. You can think of the ride stalling as being the first layer in the swiss cheese - if it didn't stall, there couldn't have been an accident. The more often the ride stalls, the more 'holes' are in the first layer of the swiss cheese, and you need more rigorous safety levels in your remaining layers of cheese -or less holes - so that the gaps don't all line up. I suspect that is what has ben going on the previous few days - beefing up those other 'layers' so that they have less holes.