Good question, force5 - you know, as I think I say on here a lot, the tricky thing about idioms is that there are thousands upon thousands of individual idiom usages in the English language so it's impossible to prepare for them all. Yes, "not only...but also" is a common idiom, but it's not the only way to use a combination of some of those words.
Here's how I'd break these apart using logic:
Not X but Y
Here, there's no "also"; it's one or the other. So you could say "It wasn't his cholesterol, but his caloric intake that caused his fitness problems." Here there's no combination of the two - there was one cause and it wasn't the one that you might have thought.
X but also Y
Here there are multiple attributes that are included together, like in that sentence above, and the second is a bit of a surprise - one should seemingly run counter to the other. "Electrons act just like other particles, but also exhibit some surprising behaviors." They have both...it's not a one-or-the-other situation. "Shaquille O'Neal was a dominant basketball player because he was massive but also surprisingly nimble and agile."
Not only X but also Y
This is fairly similar to the above, but I suppose you're more likely to use this construction when there's an add-on benefit (or detraction) from something. "My GMAT instructor wasn't only brilliant, but was also incredibly handsome," is something I've read on a lot of my student reviews...
So all three have legitimate usage, and I guess I'd put the differences as:
Not X but Y --> It's not the first thing, but instead the second
X but also Y --> the first thing is true, but somewhat surprisingly so is the second
Not only X but also Y --> You'd think the first one would be enough but the second is also true
And maybe the bigger point here is that you'll never be able to memorize every potential "correct" idiom, so I'd always recommend that you look at the major error categories first and use logic to supplement it. GMAT students so frequently like to eliminate answer choices based on idioms that the don't recognize, but just because you don't recognize it doesn't mean it's not proper.
Brian Galvin
GMAT Instructor
Chief Academic Officer
Veritas Prep
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