We had a similar thing happen at a late last year in Receipt of Invoice. Prior to the end of December 2011, Registers with a Variance would consist of 4 sections, Receipt of Invoice register, Daily Purchases Journal, Daily Purchases Tax Journal Summary and a Receipt/Invoice Variance Register.
Since December, they had been missing some Receipt/Invoice Variance Registers. Exploration showed a register with a variance will print the first two and then only the Daily Purchases Tax Journal Summary or the Receipt/Invoice Variance Register, but not both. Usually the Variance Register was the one missing.
I spent a great deal of time on this with Chris Powers and we never really got it solved. I found out that they did not use AP Tax but that it was turned on. I went through the steps to get it turned off and then with only three reports to print it did fine. Still don't have a real answer.