Signalling has changed between TRS06 and TS2009. It now knows a lot more about real signal behaviour.
A couple of examples:
Signals on plain line (with no junctions after them) are normally run as automatic signals in real life, and a signal placed in this way will become an automatic signal in TS2009. This means it does not require an approaching train to make it clear.
Signals with junctions after them are controlled signals in real life - they need a train to approach, with a route set through the signal, in order to clear. Signals placed this way in TS2009 also need an approaching train in order to clear. (Oh, and use locomotives to test this with - if you can't drive it about, why should the signalling set routes for it?).
The important thing here is that regardless of which way the points are set, if there is no train, the signal will not clear.
Both of these are intentional changes.
However, when a train approaches a junction, if the points are set correctly for a route to another signal, there is no blockage on the line (e.g. another train, then the signal should clear. It should do this early enough that the approaching train does not have to slow down significantly.*
If you have a route where a train can approach a signal, with the points set appropriately for the route ahead, and the signal does not clear, then I'd love to see it. Either post a diagram of the junction that fails, and I'll build a copy of it here, or package up the map so I can download it and see the problem.
* (Note: the TC3 semaphores have some real world behaviour where clearing is delayed until the train has nearly stopped when working within station limits. I don't believe any of these semaphores are included in TS9, so it's unlikely you are using these signals - and if you were, you'd probably have said so...)