Thanks for the comments:
I have changed the home link from .com/index.php to just .com
I have removed the link box(worldwide holiday rentals) from all pages exept the main page.
A lot of the country links from the main page have descriptions such as:
Holiday rentals france - Thousands of french holiday rentals for your summer holidays already have their own text...
The rest of the country/region links will also be getting their own text.
I did not realise that there were duplicate countries, i will remedy that.
When my site was getting page 4-6 results for the keywords I mentioned earlier it was the same as it is now (or was before I made the changes) why would it get penalised when I had not made any changes, would it not have given me results to start with?
How do I find out if Google has penalised my site? and why? so that I can fix any problems, I contacted (a couple of weeks after my keyword searches disapeared) them through the site reconsideration tool in site maps but heard nothing back (6-7) weeks ago. This was the only way I could find to get in touch with them.
Thanks for any help
Andy