A concrete example may explain...
If you go to www.voyages-sncf.com or www.raileurope.co.uk (assuming you're in the original Perth, in Scotland). Both these sites are effectively FRENCH Railways, and they naturally use the French rail ticketing system.
You try and book an ITALIAN train, Milan-Rome using the FRENCH system.
All seats on all dates are £77 / €86. Wow, megabucks.
But when you go to ITALIAN Railways' own site www.trenitalia.com, prices start at just €29 (Super-economy rate) rising to €86 (full-price).
Because the only Trenitalia fare which French Railways is allowed to sell is the full-price 'TCV' tariff advised by the Italians to the French. Rail Europe UK CANNOT sell all Trenitalia's cheap fares. Just that full-price TCV tariff.
On the other hand, if you're in Perth Australia, then you're talking about Rail Europe 4A (eg www.raileurope.com.au or www.raileurope-world.com), not Rail Europe Limited (raileurope.co.uk), they are both subsidiaries of French railways but they're separate companies, and RE 4A HAVE in fact implemented a connection to Trenitalia's ticketing system, so on RE 4A sites you may well see some of Trenitalia's cheaper fares.
So the best and safest practice is always to go directly to the relevant train operator's site, to avoid being caught out like this.
And if you use Trenitalia's site to book Trenitalia's own trains, you can choose an exact seat from a numberd seat plan - that functionality won't appear if you go through a third party. So there's another reason.
Use www.sbb.ch for Zurich-Milan.
Edited: 12:53 pm, July 24, 2013