I am currently in the process of migrating a word press site to a new server, i have uploaded the site the new server, created database, imported blogs and categories all ok!!
I have now turned the permalinks button on and chose one of the available formats, day & name. I have no problem with the index.php/ being part of the url.
However when i turn on permalinks i can not see my home page anymore, unless i specify /index.php in the url. The blog links at this point do not work either.
I am running on VPS, using IIS and plesk. The setup is exactly the same as the previous box, where permalinks worked fine.