It's called accounting! They probably use different systems.
That's silly. Accounting could account for a small difference, sure. But not one that huge. Percentage-wise, its an impressive number.
Also, both companies don't have to make money or keep a cap on losing money. Moreso, they have to give the APPEARANCE of not losing that much money. So I'm sure they both pull every accounting trick in the book.
Amtrak's capital loss is also lower, per passenger. I admit they are both pretty high. But that is, conceptually, impressive. Why? Amtrak buys cars, and they buy them new. VIA hasn't bought a new car since the LRCs. They've bought used Heritage cars and fire-sale Renn cars. But not new cars. Amtrak owns track in large quantity. I think that, excluding the class-1 freights, there is no rail operator in the country that owns more track-miles. Amtrak maintains a pair of electric rail lines of pretty high speed- especially compared to anything VIA runs.
Amtrak owns the entirety of the electric passenger lines of the old Pennsylvania railroad. They own the New Haven's electric passenger line to Springfield - even though it is no longer electrified. They own NHV-BOS. They own the Michigan City-Kalamazoo trackage.
Amtrak should be losing money hand over fist. But they don't. They cost a total of about $400,000 a year in operating expenses- $16 a passenger - and about 1.5 billion a year including their capital program - about $60 a passenger.
Via loses about $41 a passenger operating. I don't care what accounting you use. You can't accounting away 60% of the cost, especially with the government watching over your shoulder!