We have been using SL 2011 FP1 with Project Controller for years now without this problem happening. It just started for our billing in July. We have projects setup with the billing type "Bill By Task Group". There are multiple tasks in each project and each task is assigned to its own Bill Group. Most of the time only one of the tasks (per project) has a (sales) Tax ID assigned to it. Starting in July, we noticed that when we use Automatic Invoice Creation, it would create the regular lines with the correct task (and only one task) and then it would create the tax line with a different task (from the same project but does not have a tax ID associated with it and sometimes does not have a bill group assigned to it).
examples:
1. Project: RADIO. tasks: 00000 (no bill group) and 22222 (bill group = 01). Invoice is created with 22222 as the task in the regular lines and 00000 as the task in the Tax lines.
2. Project: EXALT. tasks: 11111 (no bill group), 22222 (bill group = 01), 33333 (bill group = 02), 44444 (bill group - 03), 55555 (bill group = 04). Invoice is created with 55555 as the task in the regular lines and 33333 in the tax lines.