Seems incredibly unlikely due to a few factors.
I have unlocked every single achievement at the same time for TF2 using the latest version of this tool.
I've also re-locked and re-unlocked them a few times and it hasn't banned me.
I'm sure you did something else you shouldn't have or you had the game running whilst using this tool.
If you're not running the game while you are using the tool, then there is no VAC services running to catch onto the tool.
Unless someone reports you on steam, then it's fully understandable.
Or last but not least, since the VAC3 update was released, then maybe they do have a viable way of detecting it.