I had this problem as well and though it may not help, I can tell you that:
A-This isn't really directly Toontracks fault, the verified by Visa application is a bank service.
B- I actually appreciate the extra measure of security, as my card account has been defrauded several times after online transactions.
But that said, the Verified by Visa application is flawed, and doesnt work smoothly and also, obviously it would be in merchants best interest to work with Visa to get it sorted out and working better.
The first step, is registering with Visa to use the app. In my case the primary difficulty was that the card was assigned to a joint account, and I had to use the exact, correct info to register and use the security app. This is where some method of smoothing out any issues would be very helpful. This is where Visa needs to make some changes.
Once I got that fixed, its a breeze. Just enter a password and the account is verified. Like I said, I appreciate that there is an extra layer of security. It protects the merchant and me.
And for what its worth, PayPal is not very secure. One of the problems I had was a bass boat motor someone purchased on my account, via PayPal. I have never used it since and wont.
Sorry to hear of the trouble you all are having, but thank goodness for extra security so I can comfortably shop online.