I was going to ask if its making more waste or just running slower, but then i googled reverse osmosis temperature and got this:
"The volumes listed for the reverse osmosis product water are based on a feed water temperature of 25°C (77°F). For every 1°C below 25°C (77°F), the quantity of product water is reduced by 3%. Additionally, if the feed water temperature goes beyond 35°C (95°F), the RO membrane may be damaged."
54F puts you at roughly 12C, so you are 13C below the specs, or 39% less product water is being made. Which mathematically checks out with your timing as well... (or well 40% checks out exactly to your numbers).
Math as done by google:
1/(9*60+30)*(1-.40)*(15*60+50) = 1
With units to explain:
1 gallon / (9 minutes * 60 seconds/minute + 30 seconds) * (1 - 40%) = actual product rate
Actual product rate * (15 minutes * 60 seconds/minute + 50 seconds) = 1 gallon
Alternately google math with units:
1 gallon / (9 minutes * 60 seconds/minute + 30 seconds) * (1 - 40%) * (15 minutes * 60 seconds/minute + 50 seconds) to gallon