You are not alone! I outlined my time tracking protocol here (i(Pad)OS apps: unsung heroes and new discoveries). Pertinent point from that post: I’ve built a system that automatically sets an alarm to go off after an anticipated amount of time has elapsed. Sounds like you’ve tried this already, though…
I appreciate the notion of immersion for much of the work I do, so I don’t beat myself up too much for failing to track that work accurately. I might be able to develop a clock-watching habit, but I have to wonder how much that might push an awareness of time into the foreground, to the detriment of the work I want to focus on.
Habit chaining might help here? Maybe, when you make a significant mode switch, you can build the habit of stretching or moving away from your desk for a few minutes (if your working arrangement is desk based set-up). If you can get that down, maybe that can serve as a driver for logging the next batch of activity when you return.
Also, I wonder how much resolution you might actually need for your time-tracking (as in how detailed it needs to be) and what you hope to derive from it. Are you hoping to build up to a minute by minute breakdown of the work you’ve done per day, or would it be enough just to know the different types of work or different projects you’ve given attention to?
With that said, I’m looking forward to seeing whether anyone else has a meaningful suggestion…