Updating price which is done by vmprices.js is nothing new and doesn't come with our VM Template.
All of these things are handled by Virtuemart itself. We don't override anything in vmprices.js
Any kind of JAVA conflict might cause the wrong price calculation, but i don't see any java conflict issue in your website.
But as you might guess, if issue happens randomly, It makes things harder to fix or point out the real problem. All i can provide you now is: use the latest version of Virtuemart and Virtuemart AIO.