Let's imagine that, hypothetically, the games and the cartoon are both canon. But then one thing is odd -- the Crystal Coconut that is so much more powerful than all those other crystal coconuts used as fuel for Cranky's contraptions. Well then, I will attempt to shed some light on this subject, trying to interweave all mediums gracefully. Note; this is all purely headcanons, like most things on this blog will be.
Once upon a time, far before Donkey Kong, no, even Cranky Kong was even around, far before DK Isle became colonized by Kongs who fled from the Mushroom Kingdom, Crystal Caves was blossoming. Without any cabins or buildings made by Kremlings because they didn't even knew it existed. All in all, it was undiscovered. Although it was, a certain fuel was yet to be discovered - crystal coconuts. So called because of their similarity to the nut, these orbs held so much power that they could be used to power all kinds of contraptions. There were not a lot of these around, as they all originated within caverns.
Meanwhile, the Banana Bird Queen was restlessly flying around in the hope of finding some hidden crevice in which she could lay her eggs. She found a small opening that was yet big enough to let her through and she snuck inside, finding herself in what would later be called Crystal Caves. She made a hasty little nest where she laid an unusually large amount of eggs, which would later hatch into regular banana birds, the same ones one collected in the game Donkey Kong Country 3: Dixie Kong's Double Trouble!.
Although the hatching progress was long and tiresome, a lone crystal orb rolled under the bird's body, which she barely even noticed. Of course, since the Banana Bird Queen was a mystical, magical creature, this didn't go unnoticed. Her brooding made the single coconut as magical as she was herself.
She stayed there for more than a month. (Banana bird eggs take very long to hatch.) The eggs cracked open and slowly but steadily, infant banana birds crept out. The Queen was overjoyed. She planned to nest in the hills of the Northern Kremisphere, which was at that time still a pure, unaltered wilderness, where her children could go wherever they wanted to.
At least, she thought. She didn't knew a thing about what was going to happen.
A lone Kremling pirate by the name of Captain Quint Skurvy barged into her private inner sanctum, for he knew the bird would find a nesting ground that was hidden within the Crystal Caves, and he also knew the magical powers one crystal coconut would have if it had been 'hatched' by the Queen Banana Bird. Of course, the avian didn't take this lightly. Protecting her young 'uns which she suspected the predator was after, she bit with her beak and slashed with her claws with all her might. It didn't matter in the end, for Skurvy the First was just after the Crystal Coconut. Once the prized bauble was in his possession, he fled and sailed his ship to the outskirts of DK Isle, where he hid it in the mystical idol of Inka-Dinka-Doo. The pirate blood never left the Skurvy lineage, for he was the ancestor of both Skurvy (you know, the one that sings) and Klump. But there's about a hundred years more or less between them.
Let's skip that time.
Old man Skurvy has been dead for almost a century now. Probably hung or drowned for all the crimes he'd committed. He was a pirate, after all. Donkey Kong found the Crystal Coconut which he brought to Cranky. After some investigating the simians knew enough and vowed to protect the orb. Since DK found it, he'd become the future ruler. Although Skurvy's descendant, the OTHER Skurvy, wanted the Coconut for himself because heck, it belonged to his great-great-great-grandpappy. K. Rool also wanted it, but that was because he wanted to rule DK Isle.
Later, K. Rool knew stealing the coconut was becoming a lost case. After it lost its power somehow, he went just a little bit... bananas. Thus, he stole the banana hoard Donkey Kong had been gathering for a while now. DK was pissed, so he retrieved it. The ape got kidnapped himself by K. Rool not much later. Around this time, K. Rool was seething with rage so bad that he investigated about just what made the Crystal Coconut so powerful, so he could avenge his lost time. So the King and his men stole the Queen from her bed, and bound her in her bones. Which were the clouds. The recent industrialization made the banana birds especially skittish, so of course, the brood of the Queen (that were different ones from the ones hatched in the caves all those years ago, obviously) quickly fled and became imprisoned in some crystal caverns close nearby. Only the chants of the young birds combined would be able to free the Queen from her prison.
Only later, Dixie and Kiddy freed her and retrieved her children.
She extracted her revenge on King K. Rool, who ended up hating bananas because of this exact happening.
And the Crystal Coconut? It's lost its magical powers long ago, much to Cranky's annoyance. After this, he began thinking it was all just a game someone was playing. And a crappy game, at that.
Hey. It's Cranky.