Hi,
The phenomenon you describe sounds like it's probably caused by a faulty signal linking.
Most likely it's either because of an unprotected exit, or a signal link not extending beyond the link of the opposing direction's signal. Please see this little sketch for an illustration:

On the left is the simplest junction you can do in RW. The yellow links belong to the junction signal, tpyically a 2H2T (2H2T1E if the siding is a yard lead or dead end). Link 0 is at the signal base, link 1 on the main, link 2 on the diverging track. The two siding exit signals are 1H1T, their links are colored red in this example.
On the right is what I think your junction looks like. I left out the lines between the links as this would have looked mighty confusing, but generally what you do is count the number of possible paths from each signal (which is six on the left and middle "up" track, four on the right-hand track) then place a signal with the appropriate number of track links. Always protect all possible exits of a junction, use the "E" links for yard leads and dead-end tracks. And most crucially, the siding links of each signal need to be dragged past the base (zero) link of the signals on the other side of the junction! If the link is in the middle of the crossover you can get all sorts of strange signal errors.
For the signals on the top of the right-hand side example I assumed that there aren't any slip switches in this scenario, if there were any you would have to use higher link numbers.
BTW: The number of Heads on the signal doesn't actually matter for how the signals work, this is only for visual purposes. In other words: a hypothetical 1H6T3E signal will do the same as a 3H6T3E signal in terms of gameplay and signal logic.
Hope this makes any sense.
Cheers,
Michael