Hi @bozana
An update to this issue. We did run into this with the subdomains. I have updated a new version of our mod_rewrite rules here How to remove index.php in ojs 3.0.2.0 - #15 by ajnyga. They seem to solve the problem with the api calls in subdomains.
Edit: just noticed that @paul has a similar solution above. In our case I could not get it working with a one line solution like that. The difference in our setup is that we use wildcard subdomains.
The XAMPP related problem I mentioned is occurring because of the double slash // in api url. This can be solved by adding these new lines in the mod_rewrite rules before any other rules:
RewriteCond %{REQUEST_URI} ^(.)/{2,}(.)$
RewriteRule (.*) %1/%2 [R=301,L]