I took a EuroCity from Venedig - München last sommer and encountered the Bundespolizei and Italian soldiers -(wearing some crazy hats with feathers!) at the borders.. They marched through the resto wagen to a table with two guys of Asian appearance and then promptly frog marched them from the train...
I've since read reports on the yahoo European rail gen forum that their now starting to avoid the Österreich route and go via der Schweiz, where the Grenzwache are now having fun on a nightly basis with EN 220 "Thello".. The post I read was titled "Thello to Hell!" The member wrote that the train was halted at the border for a couple of hours while a heavily armed team of Swiss Grenzwachen und Polizei promptly boarded, woke everyone up demanding passports and then proceeded to take the train apart, looking for stowaways and contraband! He said it felt more like an Interzonenzug crossing the DDR to West-Berlin from the 80's than a supposed "high quality" Western European night train in the 21st century that supposedly runs non-stop across Swiss territory from Italy to France!!!
Combined with the usual fun and frolics on Thello; air-con failed, toilets not tanked, bar not stocked, stock not cleaned, late running, loco failures and understaffing it really did sound like the trip from hell! If I remember right he wrote that he bailed at Dijon Ville hours late in the end for a TGV to Paris just to get out of the sauna that the compo had turned into and STILL got to the Gare de Lyon before the EN!
Re: The migrant issues I came across this online -(note, take quite a large pinch of salt when you read anything in this "newspaper", same applies to the daily fail!

)
http://www.express.co.uk/news/world/698331/Switzerland-new-Germany-struggle-cope-migrants-new-route
So their going through Basel and Weil now eh? That's funny as I'm in Basel fairly often and have friends there and never seen or heard any mention of migrant issues..!