I have set up a site on http://gogg.gagnavist.is and the first post on the frontpage has two links, one to a PDF file and one to a website. But the links wont appear until you click Lesa meira (read more). I have these settings under configure EXCERPTS
Excerpt length = 55
Don't strip these tags = <p><a><span><em><strong>
Then I have only excerpts in all the dropdowns below and 0 in the Show the first X posts on HOME page as full posts? field.
I´m using atahualpa 3.6.7

Can anybody help me on this ?

The reason is because of the complexity of excerpts. To build an excerpt, the code counts the words and words are defined as things between spaces. when you add '<span>' to th e'Don't strip these tags, then the span code is part of the word found (i.e. the code '<span style="font-size: small;">' counts as three words)

My suggestion is to either bump up the number of words in the excerpt or manually create the excerpt in the post.

I set the word count to 100 but nothing changed... I also removed <span> and <em> from the dont strip these tags field.

This is really strange.

you sure you still have the <a> in there?
go to ato->export/import settings and export your settings and attach them to a reply

Attached is a screenshot of this setting page and the export doc.

Try disabling your plugns to see if there is a conflint. Your settings work for me and I copied your post