My warm up routine for my silvia has been the following:

1. lock in portafilter and turn machine on
2. when heater light goes off, pull a blank shot until the heater light goes on again
3. repeat
4. repeat again,
5. grind, distribute, tamp, pull a shot

This routine has required me to switch on the pump for a few seconds just before locking the portafilter with grounds in, to get rid of overheated water. I suppose in a similar manner to an HX. In other words, the water coming out of the brew path is quite hot after this procedure. I have not measured it -- this is based only on whether it is flash-boiling when it comes out.

For the past week or so this cooling flush has been unnecessary, at least not until the machine has been on for an hour or so. In addition, the espresso has tasted more sour than usual. Everything else has been the same as usual.

Could there be some reason it is taking longer to heat up than normal? I do a descale probably two-three times per year using vinegar. The last one was just a couple of weeks ago so it could be related.

Given your description of method, the only thing that comes to mind is a brew thermostat that is opening its contact a little early in the temperature region. While this post does not exactly show when the thermostat cycles, it may be of some help - Rancilio Silvia Performance with/without PID

Do you open the steam wand at all? Could be a sticking vacuum breaker and you have false pressure in the boiler. A Silvia heats relatively quick but that looks way too fast. Turn on, wait till light goes off, open steam wand for 15 seconds, wait till light goes off again, walk away for 20 minutes then flush and continue.

I thought the Silvia used a thermostat; "false" pressure is only a factor in a pressurestat controlled machine.

My money's on the thermostat.