FooTable 3.0.1. Component loading (makes no difference if you use full script). JQuery 1.11.3. Bootstrap-CSS/JS 3.3.5 (deactivating it makes no difference)
Open http://re-later.eu/footable3-paging/footable3-paging.php
It's a table with 59 rows and default FooTable 3.0.1 settings. Only paging enabled.
<script type="text/javascript"> (function($){ $(document).ready(function(){ $("#tableselector").footable( {"paging":{"enabled":true}} ); }); })(jQuery); </script>
Do nothing and have a look at column #. It starts with rows 11 to 59.
At the end you see rows 1 to 10. This reordering is what FooTable did. Rows 11 to 59 should be hidden.
Now click paging buttons from 1 to 5, one after the other. On all pages you see this strange ordering.
But with any click there are 10 lines less.
After paging button 5 click on next pagination button with three dots.
Now pagination button 6 appears. Click it. You see the 9 last lines 51 to 59.
Afterwards you can paginate like expected.
EDIT 2015-11-01: See workaround of bertmert: https://github.com/fooplugins/FooTable/issues/371#issuecomment-152853232