Running on Linux.

I have found that removing timed traffic lights does not actually remove them, it only removes the indication that there is a timed traffic light in a junction, i.e. the stopwatch icon that appears in the junction when in TM:PE mode.

To reproduce
1. Open TM:PE and setup timed traffic light
2. Start timed traffic light
3. close TM:PE
4. Observe that timed traffic light is working
5. Open TM:PE and stop timed traffic light, and then remove timed traffic light
6. Observe that timed traffic light icon has been removed form junction
7. Close TM:PE
8. Observe that timed traffic light steps are still controlling traffic
9. Zoom into junction and observe that traffic are lights still in place and functioning

This persists through saves. The only way to remove the traffic lights is via the remove all traffic lights option in the TM:PE maintenance menu. Which as you know removes all traffic lights, not just the one that you tried to remove in step 5

I can't say when this started happening as I don't use timed traffic lights that much.