when the master page was deployed by a sandbox solution please make sure that the master page is checked in and approved. SharePoint doesn't check in and approve files that was deployed by a sandbox solution. Also make sure that the correct content type is assigned. because otherwise you won't see it too.
To set the content type of the master page on deployment correct you just need to simply add the following inside the
<Property Name="ContentType" Value="$Resources:cmscore,contenttype_masterpage_name;" />
If the master page is a farm you should also add the content type but it will be checked in automatically. I hope you are on root level of your site collection because the master page will not deployed to the sub sites.
In SharePoint Designer you also have two different approaches to find the master page.
Approach 1:
Use the Master Page Entry on the navigation pane left. The Master Page will only show up if content type ins correctly set.
Approach 2:
Go to "All Files" -> _catalogs -> masterpage
By using approach two you will see the same amount of files that you can review in SharePoint. You will also find the article pages in there.
Source: http://social.technet.microsoft.com/Forums/sharepoint/en-US/23ab5b3e-2a88-4df1-8f7e-752f4f63dfe6/deployed-custom-master-page-not-visible-in-designer?forum=sharepointgeneralprevious
