In TRS2009, try using other signals instead of the "BR" ones. Bloodnok's "2AT", "3AT" and "4AT" signals seem to work better if you want modern image, or the LMSR or GWRR semaphores. (The 2AT, 3AT and 4AT are much, much more realistic - don't forget to download the "Feather" and "Theatre" add-ons too.) Once you learn how to use these signals, you'll never look back!
I have mixed results with the "BR" range of signals in TRS2009.
If you replace the "BR" signals (which is easy to do in TRS2009 using the "Replace Assets" option, and you still have problems with low speed, it may be because you have too long a section between signals. Also, TRS2009 trains tend to anticipate the next speed limit really early.
Another problem, if you're driving someone else's route is that nthere may be a phantom speed limit in there somewhere (there are invisible speed limits on the DLS). To check this, use the Display HUD v2 Rule (on the DLS) and enable it in surveyor - it will show you what the state of the next signal is, how far away and what the next speed limit is and how far away and how far and which way the next turnout is set.
If you still have problems, I'll be flummoxed!