Would you be able to upload a savegame of the 3 track layout which doesn't work as expected?
I performed a minimalist conversion to 3 tracks and it seemed to work fine, all platforms were used.
I should point out that the current layout is prone to deadlock, as you have trains coming from the north-east which terminate at and reverse in the station, however the bidirectionally signalled tunnels permit further trains to enter from the north-east whilst the platform is occupied in a south-westerly direction, in which case the train occupying the platform would be unable to reverse and end up waiting indefinitely.
i'd say it's a problem with the "signals in tunnel", which is notoriously unfinished and doesn't behave properly in combination with path signals.
i don't understand how anyone could ever use that patch. in any case, make sure there is at least one block signal before and after such a signals-in-tunnel section
The implementation which is included in the patchpack is not the same as the various patches posted on these forums.