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How to navigate the murky world of credit scores

FORTUNE — This column started — as many do — with a question from a reader. It ended in a place I didn’t expect. As I followed the breadcrumbs and figured out what was going on in my reader’s case specifically (which you’ll read about in a minute), I learned about something dragging down the credit scores of the millennial generation in general. Both were interesting. So, this week kicks off a two-parter on what’s happening in the world of credit scoring (and what you can do about it.).

Topic 1: Your Many, Many Credit Scores

So … back to my reader, a 40-year-old small business owner with a nice six-figure income living in the Northeast. She had been contacted by both her mortgage lender and the holder of her home equity loan and invited (by both, separately) to refinance, roll two into one, and lower her combined interest rate. That sounded good so she applied to her mortgage lender. In short order, she was denied. The reason: her credit score, which the lender said was an Experian score of 630. In the world of credit scores, this is fair bordering on poor.

My reader figured this had to be a mistake. Before applying she had done what many responsible consumers would do — she checked her credit score herself. For several years, she’d been paying $16.95 a month to TransUnion, one of the three major credit bureaus, for credit monitoring. From this service, she pulled a report detailing all three of her scores — one from each of the bureaus. They were all in the mid-700s.

So she applied again, this time to the holder of her home equity loan. Again, she was denied. This time the reason cited was an Experian score of 650.

How was it possible, she wanted to know, for her scores to be so all over the place? Some consumers already know they have more than one credit score. Many believe they have three — one based upon the credit reporting data from each of the major credit bureaus: Experian, TransUnion and Equifax (EFX). In fact, says John Ulzheimer, education expert at, you have more than 50. (Yes, that’s 50 — as in five-oh.)

Most of these are various FICO scores, sliced and diced by FICO (formerly Fair, Isaac and Co.) to give lenders the information they want to use to make decisions about whether or not to give you money. Auto lenders, for instance, want to see information about how you’ve repaid prior car loans. Ditto for mortgage lenders, credit card companies, and insurance companies regarding their individual universes. Multiply each of these by the number of bureaus, and by iterations of the FICO score (think versions, like software) and you can start to see how the numbers add up. And that’s just FICO. A newer company, Vantage Score, started by the bureaus themselves to compete with FICO, has captured somewhere between 5% and 10% of the market according to Ulzheimer. It has multiple versions, too.

All of which is interesting. Frustratingly though, very few of these versions are actually available for you to see. That’s problematic for the consumers whose online scores tell a story so different about their risk than the scores lenders see that it bumps them from “Good” to “Fair” or “Fair” to “Poor” and results in them being charged a higher rate of interest or turned down entirely. How often does this happen? Customers are moved one scoring category about 20% to 25% of the time, according to a 2012 report by the Consumer Financial Protection Bureau.

What happened to my reader, however, was something different. What the lenders saw when they checked her credit were versions of her FICO score. What she saw when she pulled her own scores from TransUnion were Vantage Scores. FICO scores range from 300 to 850. Until the release of Vantage Score 3.0 in 2013, Vantage operated on a scale of 501 to 990. And, just like some Mac computer users are still running Snow Leopard, some users of the Vantage Score — including TransUnion — are still running the prior versions.

Makes you want to pull out your hair, doesn’t it? It did that and more to my reader. It cost her hours of her time (including the time she spent communicating with me and the time putting together the two loan applications). It cost her money (for that subscription, which she has since cancelled). And it cost her inquiries on her credit report that took her already wobbly credit score down a notch or two.

Bottom line: What can you do about this? Ulzheimer and Maxine Sweet, who leads consumer education at Experian, basically have the same message: Control what you can control. “There’s no such thing as improving your score,” says Sweet. “What you can do is improve your behavior.” That means, pay your bills on time every time, don’t use more than 30% of the credit you have available to you on any one card in particular or all your cards combined, don’t apply for credit you don’t need and don’t close old cards in haste. By doing this, you’re essentially managing the information that goes on your three credit reports. Every single one of your scores is based on the information on your three credit reports. And it’s a lot easier to manage three credit reports than it is to manage all of those scores. “If you have good credit then you’re going to have good scores regardless of the model,” says Ulzheimer. “That’s what’s guaranteed.”

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