Installing and upgrading help

Jason,
The bug you see in array_key_exists() is because the second parameter sent to the function is not always an array, its sometimes NULL I think!
But as yet I can't figure whether that's the navigation algorithm's fault or the data after conversion... I get the same bug. And I'm now leaning heavily towards the idea that its the data!
I can get rid of the bug by wrapping the two sections (that line and higher up) that make the call to array_key_exists() with
if (!empty($parentref['children'])) {
/// call here
}

Like this...

foreach ($parents as $parent) {
// test added to remove bug
if (!empty($parentref['children'])) {
if (!array_key_exists($parent, $parentref['children'])) {
$parentref['children'][$parent] = array('category'=>$categories[$parent], 'children'=>array());
}

$parentref = &$parentref['children'][$parent];
}
}
// test added to remove bug
if (!empty($parentref['children'])) {
if (!array_key_exists($category->id, $parentref['children'])) {
$parentref['children'][$category->id] = array('category'=>$category, 'children'=>array());
}
}

But I don't know what harm I'm masking with this, and I think it makes the navigator behave strangely!! HOWEVER, I think a big clue could be in the existence of a non-standard block or more likely activity pre-exisiting in 1.9+ before your upgrade, that you have not been able to upgrade the code for because that code doesn't yet exist!

I'll explore this idea a bit further with my own troubled dataset!

John