As far as I know they cannot dig any deeper than what you provide them. The only way anyone could ever know you worked somewhere is by either calling that place or figuring out where you worked from your tax return. The IRS does not give out information to just anyone who asks for it. Even if they seek out the IRS, got that you are working at your current company, they'd still have to get someone to call there to determine how long you worked there. What would that even tell them?
With that said, a background check does the following: verifies your employment history that you provided, verify education you provided, does a special kind of credit check to see if you missed payments after 30 days or if you owe money, checks criminal background with state and federal levels. They may also call references you provided but I rarely hear of this happening. At my last private employment, my background check process came back in 48 hours.
They don't send out an investigator as that will cost a lot of money for the investigation company. Now there are some exceptions like if you're trying to get a security clearance or if you work for the bank or nuclear power grid. They do a different type of investigation but a typical company isn't going to dig any deeper than what you provided them.
Edit: Not that I'm saying you should be untruthful. I'm just saying at a private company they can only do so much as they are limited by money and time. Do they want to spend $1000s of dollars to a background company to dig out your entire life story? It's about a risk factor and if they can cover what they believe are risk factors, then that is good enough. You should always be truthful and never lie about your history, however small in detail as that may come up later. If they find out you made a small lie on a previous employer, they will begin to ask themselves if you can be untruthful about something small, what else?
And that finding may not be from a background check. Maybe a co-worker from that company becomes a manager at your place. He's like, "Oh yeah, I know him he worked where I was for 6 months last year." Then someone says, "Hold on, I thought he was off on vacation. Let me dig into this somemore."