I've been looking to fix this issue for a while now.
I have a visualforce page and a custom action for account. I added the action in the page layout. If I go to the salesforce 1 app with the browser on the computer (https://na10.salesforce.com/one/one.app) or in the phone and use that action, the custom page is only shown in a little space at the top of the page. It doesn't happen in the native salesforce 1 app for android.
It's the same in Chrome and Firefox.
I followed the steps in chapter 12 of https://developer.salesforce.com/docs/atlas.en-us.salesforce1.meta/salesforce1/salesforce1_guide_intro_set_up_org.htm