Nice rolling stock! The weathered wood, like on the gondola, looks very good!
I've still troubles while applieing decals so I hope that a soft weathering will hide most of the disaster.
I don't know what sort of decals you use. It looks like they are a bit thick and stiff, am I right?
Microcale Set & Sol helps with aplying most decals. It soften the decals a bit and help it to set correct on the surface (and prevents the whitening).
Anyway, you allready have the decals on, so this it talking afterwards...
If I had this problem I would try a coat of clear paint (or Future) over it. This to prevent the decals from the washes of paint when you start weathering the cars (for instance the thinned paint flowing under the decals or rapture them by drybrush).
After this coat is applied you can weather it safely. Sometimes the whitening even dissapeares (or is less showing) when using Future (but as I said: sometimes!). Future has an egg gloss, so it has to be matted down again. But that's no problem when you are weathering the cars.