Signal Tap inverting the Bits

When a register must power-up high, synthesis will do something not-gate pushback. In essence, the register will still power-up low, and a not-gate will be put before and after it(and not gates can absorbed into LUTs for free, so there's generally no cost in doing this.) From a system level, this has the exact same behavior, but if you tap the actual register, you're tapping right before the not-gate after it, and it will look like it's the opposite of what it should be.

The Synthesis report should have a list of all registers inverted, although it caps how many it reports to 100. This cap can be increased under Assignments -> Settings -> Analysis and Synthesis -> More Settings -> Number of Inverted Registers Reported...

Personally, I would prefer to have the name slightly changed, like a ~inv added to the end, or something like that, so I don't have to go to a list. (Actually, once you've spent time looking at it, you get used to it and realize this occurs without going to the list). File an SR for this change if you'd like it too.