I was able to duplicate the behavior you described. Thank you for the feedback. Improvements are on the way.
In the mean time, you should be able to work around the issue. The details depend on what you want to do.
A) rename the tab for the uk table page (uk.htm) to be 'United Kingdom'
B) create an additional tab and page for the uk table
If you just want to rename the tab for qid/table 'uk':
1. use PageGen to generate the basis page for qid/table 'uk' as 'united_kingdom.htm'
2. add a customization element (to custom.inc.php) for the tab:
$this->m_data[APPID]['countries'][INCL][NAV][] = array(A_HREF=>'united_kingdom', A_TEXT=>'United Kingdom');
* OR *
$this->m_data[APPID]['countries'][INCL][NAV] = 'united_kingdom';
3. delete the Basis Page file 'uk.htm' (or it will continue to appear with a NAV tab) (the same is true for uk_report.htm)
If you want an additional page for qid/table 'uk':
1. use Tools/QueryID to define a Secondary QueryID 'united_kingdom' for Basis QueryID 'uk'
2. use PageGen to generate a Basis Page (and/or) Report Page for qid/table 'united_kingdom (uk)'
You could use the Secondary QueryID technique to just create renamed NAV/RPT tabs, pages and reports from the outset. But, if you've used PageGen to generate a Basis Page and/or Report Page for a default qid/table, then you'll have to clear the Basis Page and/or Report Page check box(es) and Run PageGen again, to record the settings, and prevent the page/report from being re-generated. Delete the corresponding default qid/table Basis Page and/or Report Page (.htm file(s) to get rid of the pages (and tabs).
So, I'll work on the INCL/OMIT behavior while you see if you can use the suggestions to get your application working the way you want.
-Richard