After upgrading to 3.16.5 in Ubuntu 15.04/Wily Evo started to experience periodic freezes for a few seconds at a time.

The file filters.xml was found to contain entries like these:
    <rule enabled="true" grouping="any" source="incoming">
      <title>Retail</title>
      <partset>
        <part name="sender">
          <value name="sender-type" type="option" value="contains"/>
          <value name="sender" type="string" allow-empty="true">
--->        <string>@MYHABIT.com</string>
--->         <string>@MYHABIT.com</string>
--->         <string>@MYHABIT.com</string>
            ....
          </value>
        </part>
        <part name="sender">
          <value name="sender-type" type="option" value="contains"/>
          <value name="sender" type="string" allow-empty="true">
--->         <string>store_news@amazon.com</string>
--->         <string>store_news@amazon.com</string>
--->         <string>store_news@amazon.com</string>
            ...
          </value>
        </part>

In some of the nodes the string tag was repeated up to 16384 times.

Slowdowns are gone after filtering out the duplicates in the file.