Many (most?) business keep two sets of accounting records. One for taxes, and one for investors/banks/executives/etc. The accounting standards for taxes are different than for US GAAP, which is the accounting standard for businesses.
One area that would make a very significant difference is in depreciation. For tax purposes, you refer to the MACRS schedule for how long to depreciate your assets. For property, I believe it's 27.5 years or 39 years (up to you). Under US GAAP, however, you determine the useful life of the asset based on how long you think it will last. The most common I've seen is 40 years, but if you owned a skyscraper in Manhattan I could understand the justification of something longer, maybe even 100 years.
The math looks like this:
Assume you purchased a $100,000 property. For taxes, your annual depreciation expense will be ($100,000/27.5) = $3,636.36. For US GAAP, it's ($100,000/40) = $2,500. So for the IRS, you just lost over $1,000 more in the year.
Also, depreciation is a concept; you don't actually pay for depreciation directly. That's why you can have positive cash flow and still sustain book losses.
Other similar concepts that reduce profits without impacting cash flow are accruals for maintenance and repair, capex accruals, vacancy accruals, etc.