We have a similar problem with an Alfresco server (3.4 version) behind a BlueCoat reverse-proxy.
Everything works fine for months, but when we use Alfresco App 1.2.1.32 on ipad on iOS 5.0.1, it is possible to get the activities and to browse the sites, but it is always inpossible to get a document.
After strong investigations and looking at the packets between Alfresco/reverse-proxy and ipad, we discovered that the Alfresco App seems to deal properly with SSL for most request EXCEPT when it tries to reach a document where the request is not crypted.
Consequently, the document request is not accepted by the reverse-proxy (whose role is to reject all improper or suspicious requests).
So, it seems that there's no way to get a document on the mobile if your Alfresco is behind a proxy-server, until next release of Mobile Alfresco App.
Marc Le Bris
Conseil Régional du Centre
F-45000 Orléans - France