The persistent, often repeated fallacy that the dust cap does not keep out water on a first stage rears it's ugly head once more. It's simply wrong, as long as the dust cap is in good shape. Keeping water out is EXACTLY what it is designed to do. Man do people overthink this.
However, for the ultra paranoid among us, there is a very simple test to determine if your dust cap is sealing. Simply install it and try sucking some air out of the 2nd stage. No air? Everything is fine. Air? There's a leak somewhere. It could be in the 2nd stage you are sucking on, or it's possible if the reg has a seat saver function on the other 2nd stage, air could come in there and travel through the hose into the IP chamber and back out the hose attached to the stage in your mouth. Or, the final possibility is that the dust cap is leaking. In my 20 years of working on regulators I have never once found a leak from a decent quality dust cap that is not damaged. (like one of the older style missing an o-ring, or a crack)
If you're still reading (sorry for the long post) and want to further track down the source of the vacuum leak, the first thing is to try the other 2nd stage. No air? It must have been the seat saver or a leaky 2nd stage. Air? Try putting the reg on a tank, keep the valve turned off. (I think we can all agree that the tank provides a good seal, can't we?) Try again, both 2nd stages. No more air? Your dust cap needs replacing. Still getting air? You definitely have a 2nd stage leak. Sometimes there is a seat saver is the primary, meaning you can draw air through the alternate, but also a leaky exhaust valve or mouthpiece in the primary.