If you stopped the correct train causing the lock, the junction would release. Sometimes the junction-locking train is elusive and you need to search further than what trains are in the vicinity, particularly on a long mainline. (This of course assumes a train is not stopped near the junction).
In my experience this crops up when a mainline is too train-loaded to have single-tracked portions. As an example, if we took the Mojave route supplied with TS12 (which has several single to double track transitions along the main line) and overloaded the mainline with too much traffic, we would get the problem you describe. The remedies are to make the line double-tracked or to reduce the traffic. This may or may not be your case, I don't see enough detail to pinpoint your remedy.
The command you speak of is for TRS2006, is there any proof it works for TS12 (assumed from your registration banner)?