2006 Honda Civic Hybrid -- starting problems if not recently (12hours!) driven

Question

I have a 2006 Honda Civic Hybrid. About a year ago, I noticed it had starting problems if not recently driven in the last few days, like when I'd come back from a vacation or if I didn't drive it during a 3-day weekend. Normally it starts almost instantly; in this case the starter would take a second or two before the engine would catch, initially starting with what seemed like a backfire. My mechanic couldn't figure out anything wrong.

The problem has continued and the "recently" time period has shrunk, now it is about 12 hours or so. I get home at night around 6pm and leave for work around 7:30am, and each time in the morning it has this problem. When I go home it doesn't have the problem. (It's not a temperature issue as far as I can tell; we live in a warm climate and I've had the same problem often when starting during the weekend at midday.)

Does anyone know what it might be + what I should ask my mechanic to look at? I wonder if it is a leak of some sort into the cylinders.

(Just to clear up the obvious question, the starter motor works every time, it just takes a while for the engine to engage.)

Clarifications:

Cranking isn't slow (so the battery doesn't seem like the problem)
I get a slight hydrocarbon smell after this "bad startup" occurs (fuel or oil maybe?)
(possibly unrelated issue) When I come to a stop and have my foot on the brake, e.g. at a red light, the engine is supposed to automatically stop and then restart when I take my foot off the brake. It no longer does this, instead it remains idling in the 500-1000RPM range.

Noted conditions when starting after a 36-hour downtime period: engine sputtered for about 1.5 seconds, then started. During this time starter did not slow down appreciably, but had to work very hard and pulled down the starting battery just enough to trip the low-battery light (which went off a few minutes later). (The 12V battery is somewhere between 18-24 months old + seems fine otherwise.)

Alex C · Accepted Answer

When I come to a stop and have my foot on the brake, e.g. at a red light, the engine is supposed to automatically stop and then restart when I take my foot off the brake. It no longer does this, instead it remains idling

This is an indication that the battery or electrical charging system is not in an optimal condition, most likely the battery in particular.  If it has aged enough, regardless the number of months since you bought it, it can no longer hold the same charge. It may have very well sat on a shelf for X years before being sold.
Start/Stop systems are designed to stop the car only when a series of conditions are met, and the most important one is for the battery capacity to reach a certain threshold, which varies from model to model. If, after you changed the battery, start/stop did not work at all anymore, then it may be because the battery is not suitable for your system (google for BEM code).

The problem has continued and the "recently" time period has shrunk

This is the second thing that points out a possible old battery. For what I know, for the engine to fire, it is necessary for the starter to reach a certain rotation speed, otherwise on some gasoline cars there may not be any spark at all, which prevents detonation. There may also be other reasons that prevent the spark, which I'm not aware of.
Once again, if the battery isn't in it's best state, the necessary rotation speed will be reached during a longer period of time as the electrical engine is not able to draw the necessary current from the old battery.
I would save myself the trouble and just go to a specialized battery shop where they have a special tool that tells you how much capacity your battery still has, as well as diagnose other possible electrical issues.
It's usually cheap and very effective.

2006 Honda Civic Hybrid -- starting problems if not recently (12hours!) driven

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