It's essential that your hand-built turnouts get "de-burred" as I like to call it. This means that when you cut the gaps in the cladding on your PCB ties, you make sure there are no little burrs left (especially on the vertical edges) that can later bend and short across the gaps in the cladding copper. Sometimes a shard of rail material will lodge in a freshly cut rail gap...also causing a short. I use a small welding brass or steel brush I buy at Harbor Freight to get rid of any burrs and shards while the turnout is still on the bench.
However, I NEVER rely on what I can see, and I ALWAYS use a voltmeter to test for electrical correctness while the turnout is still on the bench.
Before I install ANY turnout onto my layout...before any feeders are soldered to it, I test it thoroughly for shorts, using a voltmeter, making sure that (A) both stock rails are totally isolated from each other, that (B) both closure point rails are totally isolated from each other, but are (C) connected electrically to the adjacent stock rails, (D) that the frog is totally isolated from all the rails, and that the frog rails are (E) isolated from each other, the frog, and from their adjacent stock rails.
It's handy to solder feeders to your PCB ties, but excess solder can sometimes bridge the gap between upper and lower cladding on the PCB ties, especially if there are both + and - feeders attached to the same PCB tie. This can cause phantom shorts that are very difficult to find and resolve (don't ask me how I know this!), especially if you run the feeders up through holes drilled in them, or you form a 90 deg. angle in your feeder wire and fit the vertical part pressed tightly against one edge of the PCB tie. It's easy for solder to adhere to the underside cladding and you'll get a short if the bottom cladding isn't also gapped. Cut the gaps in the top and bottom cladding at different points on the PCB tie so both gaps are not stacked on top of each other which will weaken the PCB tie. It's easy to run several feeders off of one long PCB tie...including the frog feeder...and this makes for neat electrical connections. Just make sure (once again) that you've gapped the bottom cladding on the PCB tie you're attaching different polarity wires to and/or through.
Remember, you don't have to remove ANY of the material that's under the copper cladding to get an excellent gap, nor do you have to run all the gaps down the center of the ties, which will draw your eye very quickly and look quite unprototypical for gaps cut into the top of the ties. For gaps cut into the bottom, who cares what they look like??
Now for a few questions: (1) - Did you check your turnout for electrical problems before your installed it using a voltmeter? (2) - Have you checked your turnout for electrical polarity problems after it's installed (feeders soldered to it) using a voltmeter? (3) - Does your engine "cause" the short, or does it just venture on to a piece of rail that's the wrong polarity when it crosses the gap?
Most likely you've got a rail that's the wrong polarity which is insulated from the preceding rail by the gap, and when the engine's wheel crosses the gap...it closes the circuit and "finds" the rail that's the wrong polarity...causing a short.
An easy way to find if you've got a rail that's the wrong polarity on one side of a gap is to bridge the gap with a voltmeter probe, or the blade of a small screwdriver. if you insert the probe into the gap, and it shorts, then the rail your engine is traveling into is the wrong polarity and it needs to be corrected.
Remember, it's pretty handy to solder feeders to your PCB ties, but...don't make it a practice to solder both + and - feeders to the same PCB tie, unless it's gapped on the bottom too.
You might have one of these phantom shorts, but it sounds like you've just got one rail wired incorrectly.
GOOD LUCK!
Bob Gilmore