When you left click on the physical input, you turn ON the internal bit that represent the input status and when you let go the left mouse button it will write an OFF to the bit. So if you click on the input and then let go the mouse button when the CPU is busily running inside a custom function, then the input change may not be seen by the CPU. Try holding on to the mouse button and see if the timer will be initiated correctly.
Note that when you press on the left mouse button the bit representing the input is changed asynchronously. i.e. it can happen at any time during the ladder logic scan, and the internal input bit will be overwritten by the state of the actual physical input when the CPU perform the I/O scan. So it depends on when the change of the input take place the CPU may still miss the input change if the CPU is waiting in a loop somewhere inside a custom function.
If you want to activate a timer from online monitoring, it is better to turn on an internal relay and connect the internal relay's contact in parallel to the physical input. This will ensure that the relay state change will activate the timer. The relay state can be turned OFF by the program when the related function or timer has begun operation.
