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Category Order could not understand your category HTML. Please do the following:

Disable all plugins except for category order to see if some other plugin is causing the problem. If the problem goes away, re-enable each plugin until you find the incompatible one.
Try switching to a different theme, like the WordPress default theme.

Once you have tried the above steps, email david@coppit.org with the results of these debugging steps. Also include the following information:

Original HTML:
<li class="cat-item cat-item-1"><a href="https://blogs.bootsnall.com/Jonnie-J/category/1" >1</a> (16)
</li>
<li class="cat-item cat-item-104"><a href="https://blogs.bootsnall.com/Jonnie-J/category/chicago" >Chicago</a> (1)
</li>
<li class="cat-item cat-item-203"><a href="https://blogs.bootsnall.com/Jonnie-J/category/colorado" >Colorado</a> (2)
</li>
<li class="cat-item cat-item-1590"><a href="https://blogs.bootsnall.com/Jonnie-J/category/ecuador" >Ecuador</a> (5)
</li>
<li class="cat-item cat-item-2487"><a href="https://blogs.bootsnall.com/Jonnie-J/category/music" >Music</a> (1)
</li>
<li class="cat-item cat-item-5866"><a href="https://blogs.bootsnall.com/Jonnie-J/category/the-grand-lake-lodge" >The Grand Lake Lodge</a> (3)
</li>
<li class="cat-item cat-item-1559"><a href="https://blogs.bootsnall.com/Jonnie-J/category/the-plan" >The Plan</a> (2)
</li>
<li class="cat-item cat-item-132"><a href="https://blogs.bootsnall.com/Jonnie-J/category/travel" >Travel</a> (61)
</li>
<li class="cat-item cat-item-5865"><a href="https://blogs.bootsnall.com/Jonnie-J/category/travels-with-joel" >Travels with Joel</a> (1)
</li>
<li class="cat-item cat-item-5867"><a href="https://blogs.bootsnall.com/Jonnie-J/category/volunteer-stuff" >volunteer stuff</a> (1)
</li>
<li class="cat-item cat-item-5869"><a href="https://blogs.bootsnall.com/Jonnie-J/category/what-i-dig" >What I dig</a> (1)
</li>
<li class="cat-item cat-item-5870"><a href="https://blogs.bootsnall.com/Jonnie-J/category/where-ya-been" >Where ya Been?</a> (1)
</li>

Processed HTML:
<li class="cat-item cat-item-1"><a href="https://blogs.bootsnall.com/Jonnie-J/category/1" >1</a> (16)
</li>
<li class="cat-item cat-item-104"><a href="https://blogs.bootsnall.com/Jonnie-J/category/chicago" >Chicago</a> (1)
</li>
<li class="cat-item cat-item-203"><a href="https://blogs.bootsnall.com/Jonnie-J/category/colorado" >Colorado</a> (2)
</li>
<li class="cat-item cat-item-1590"><a href="https://blogs.bootsnall.com/Jonnie-J/category/ecuador" >Ecuador</a> (5)
</li>
<li class="cat-item cat-item-2487"><a href="https://blogs.bootsnall.com/Jonnie-J/category/music" >Music</a> (1)
</li>
<li class="cat-item cat-item-5866"><a href="https://blogs.bootsnall.com/Jonnie-J/category/the-grand-lake-lodge" >The Grand Lake Lodge</a> (3)
</li>
<li class="cat-item cat-item-1559"><a href="https://blogs.bootsnall.com/Jonnie-J/category/the-plan" >The Plan</a> (2)
</li>
<li class="cat-item cat-item-132"><a href="https://blogs.bootsnall.com/Jonnie-J/category/travel" >Travel</a> (61)
</li>
<li class="cat-item cat-item-5865"><a href="https://blogs.bootsnall.com/Jonnie-J/category/travels-with-joel" >Travels with Joel</a> (1)
</li>
<li class="cat-item cat-item-5867"><a href="https://blogs.bootsnall.com/Jonnie-J/category/volunteer-stuff" >volunteer stuff</a> (1)
</li>
<li class="cat-item cat-item-5869"><a href="https://blogs.bootsnall.com/Jonnie-J/category/what-i-dig" >What I dig</a> (1)
</li>
<li class="cat-item cat-item-5870"><a href="https://blogs.bootsnall.com/Jonnie-J/category/where-ya-been" >Where ya Been?</a> (1)
</li>

Category pattern:
/http\:\/\/blogs\.bootsnall\.com\/Jonnie\-J.*?\/category\/(?:[^\/"]+\/)*([^\/"]+)/

Items:
Array
(
    [0] => <li class="cat-item cat-item-1"><a href="https://blogs.bootsnall.com/Jonnie-J/category/1" >1</a> (16) </li>
    [1] => <li class="cat-item cat-item-104"><a href="https://blogs.bootsnall.com/Jonnie-J/category/chicago" >Chicago</a> (1) </li>
    [2] => <li class="cat-item cat-item-203"><a href="https://blogs.bootsnall.com/Jonnie-J/category/colorado" >Colorado</a> (2) </li>
    [3] => <li class="cat-item cat-item-1590"><a href="https://blogs.bootsnall.com/Jonnie-J/category/ecuador" >Ecuador</a> (5) </li>
    [4] => <li class="cat-item cat-item-2487"><a href="https://blogs.bootsnall.com/Jonnie-J/category/music" >Music</a> (1) </li>
    [5] => <li class="cat-item cat-item-5866"><a href="https://blogs.bootsnall.com/Jonnie-J/category/the-grand-lake-lodge" >The Grand Lake Lodge</a> (3) </li>
    [6] => <li class="cat-item cat-item-1559"><a href="https://blogs.bootsnall.com/Jonnie-J/category/the-plan" >The Plan</a> (2) </li>
    [7] => <li class="cat-item cat-item-132"><a href="https://blogs.bootsnall.com/Jonnie-J/category/travel" >Travel</a> (61) </li>
    [8] => <li class="cat-item cat-item-5865"><a href="https://blogs.bootsnall.com/Jonnie-J/category/travels-with-joel" >Travels with Joel</a> (1) </li>
    [9] => <li class="cat-item cat-item-5867"><a href="https://blogs.bootsnall.com/Jonnie-J/category/volunteer-stuff" >volunteer stuff</a> (1) </li>
    [10] => <li class="cat-item cat-item-5869"><a href="https://blogs.bootsnall.com/Jonnie-J/category/what-i-dig" >What I dig</a> (1) </li>
    [11] => <li class="cat-item cat-item-5870"><a href="https://blogs.bootsnall.com/Jonnie-J/category/where-ya-been" >Where ya Been?</a> (1) </li>
)