Yes, some carriers use different routing programs that amazingly pay you less miles than the practical route programs. The first two companies I was leased to seldom paid what the actual mileage was...not even close. 10% short was probably a good average. I heard all of the same excuses over and over again just like your hearing here. I moved to an honest carrier and magicly, the miles are accurate now. I seldom loose more than 5 maybe 10 miles and at times I can even run the load in LESS miles than I'm paid. We have one load from Oak Creek, WI to Springfirld, OH that actually pays 10% MORE miles than what it takes to drive it. Imagine that? You can bet your azz that your carrier is not getting paid on short miles...only you....IMHO.
When you decide to change carriers don't believe anything the carrier or their drivers tell you about mileage pay. The carrier has all the excuses and the drivers believe them. Talk to a couple of drivers and just ask them how accurate their miles seem to be. If they start with the excuses that your hearing now, their getting shorted and don't know any better.
Miles should be accurate. Miles can be accurate. Anybody who is not being paid accurate miles is being shorted miles.