That's really interesting Paul - I've noticed a very similar problem on 
instances which aren't "Always On" but haven't been recycled (reported at 
this 
Link<https://groups.google.com/d/msg/google-appengine/VEifURis4OI/-kmdlQh7AXgJ>
)

I've noticed the following CPU costs to my app when it's left idle and the 
instances haven't been recycled:

Normal cost = ~200cpu_ms
20mins = ~750cpu_ms
1hr = ~1200cpu_ms
4hrs = 5000cpu_ms
8hrs = ~12-13000cpu_ms
>12hrs = ~30-45000cpu_ms

This CPU cost can be found on any resources, whether they are static or 
dynamic - it's always triggered on the first request to a particular 
instance.

Depending on how many instances haven't been recycled, this can lead to an 
initial burst of cost which blows a decent bit of the quota for very little 
gain!  It's actually cheaper, CPU-wise, to not have the instance there and 
have a warm-up request instead.

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