Alpha SY24, Timer does not always switch it off?

Boiler appears to be running fine. Cuts in and out as water temp requires but system does not always switch off when the timer tells it to. There's a TP Ikon seperate programmer. System has no room thermostats. Has normal motorised valves etc. If I turn boiler switch to 'frost' or just to off it duly obeys. If not alight at the time the timer goes off it appears to do the job normally. If the timer sends its off command when the burners are operating the boiler appears to ignore it and carries on.