I reported this months ago, but it seems to keep falling off the to-do list...
If you select "Level %" (that's Level PERCENT, not just Level) and then click on "Save Sorting", it says "Characters now set to sort by the LEVEL column". And it does just that - sorts by the LEVEL column instead of the LEVEL PERCENT column.
This problem is caused by the wrong ID being used on the column header label:
<thead>
<tr>
<th id="faction">Fac</th>
<th id="origin">Or</th>
<th id="archetype">Ar</th>
<th id="hidden">Hide</th>
<th id="image">Img</th>
<th id="flag">Flag</th>
<th id="name">Name</th>
<th id="level">Level</th>
<th id="server">Server</th>
<th id="primary">Primary</th>
<th id="secondary">Secondary</th>
<th id="offline">Days Offline</th>
<th id="level">Lvl %</th>
<th id="badges">Badges</th>
<th>Actions</th>
</tr>
</thead>
Fixing that typo may not fix the problem, but it is definitely a start...