Corporate tax inversions have been in the spotlight as a controversial strategy used by U.S. companies to ease the burden of the country's 35-percent corporate tax rate.

Typically, an inversion results when a U.S. firm acquires a foreign firm, and in the process of the transaction, reincorporates so that the foreign firm is the parent company and the U.S. firm is a subsidiary. Once the foreign firm becomes the official headquarters, the combined company no longer owes U.S. taxes on income earned overseas, a significant benefit given the high U.S. corporate tax rate.

Sounds like a sweet deal, especially if you're a shareholder in one of these corporations, right? Therein lies the rub. While a vast majority of shareholders get a huge benefit on an inversion deal, some are learning that an inversion isn't always in their best interest.

A recent research paper shed some light on this phenomenon by studying 60 inversions by U.S. public companies over the last 20 years. The two-decade time horizon was significant because it captured transactions that occurred after legislation designed to discourage inversions by requiring stockholders to pay capital gains taxes on their shares at the time of the inversion.

The study found that these capital gains taxes make inversions particularly unattractive for long-term taxable investors who have seen their shares appreciate significantly over the years. For example, the paper's authors explain, investors who bought Pfizer five years ago have seen their shares appreciate by 80 percent, while investors who bought 25 years ago have seen their shares grow by six times (adjusted for splits). In the study sample of 60 different inversion deals, approximately 15-20 percent of shareholders fell into this long-term investor category and were made worse off from the inversion.

Oliver Levine, an Assistant Professor in Finance, and the Patrick A. Thiele Fellow in Finance, at the Wisconsin School of Business, and Brent Glover, an Assistant Professor of Finance at Carnegie Mellon University, are two of the authors behind this paper, and I recently had a chance to speak to them about their research.

"This is an unusual situation, because the benefits vary across individual shareholders, as opposed to most corporate actions, where there is uniformity in what the best policy is. In these cases, we don't have that," Levine said.

In fact, while long-term taxable investors who've seen their shares appreciate over many years tend to lose money on an inversion deal, tax exempt and tax deferred investors - such as those investing in company stock through retirement accounts, pensions, endowments, 401(k)s and IRA accounts - tend to see gains on the order of 4-7 percent following an inversion.

"We're in an interesting period where such a large chunk of investible assets is being held in tax-free accounts, so the bulk lot of investors only share in the benefits of an inversion deal," Levine continued. "So we're talking about a significant minority of these shareholders that would incur these capital gains."

So with one group of shareholders essentially writing a very large check to the government for all shareholders to reap the benefits of lower corporate income taxes in the future, it begs the question: Are the shareholders who are most at risk in an inversion scenario even aware of this disadvantage?

"There are certainly instances where shareholders have been aware of this; in fact we've heard from some after publishing our research," Glover explained. "But it is worth noting that although some shareholders may be made off worse by the inversion, it's value-increasing for others. So the fiduciary responsibility to shareholders can be tricky to evaluate in these cases.

I asked the two how the U.S. can ease corporate tax inversions as a whole, and there seems to be no perfect silver bullet.

"There are two broad approaches the government can take. One is to treat U.S. corporations the same as foreign corporations. You could no longer have a worldwide taxation system, and then profits are taxed wherever they're earned. But if you don't have worldwide taxation, you have an incentive to profit shift to a lower tax jurisdiction. The other is you can reduce the corporate tax rate, but of course the downside of that is reduced tax revenue. So there's no perfect solution."

With new rules enacted by the U.S. Treasury that go a long way in discouraging these types of deals, it certainly appears that stopping inversions is the way the government wants to go. And if there isn't a willingness to trim that capital gains burden, it seems like these 15-to-20-percent of shareholders caught between a rock and a hard place are destined to continue to feel the squeeze.