I have had various difficulties with PowerPivot files in SharePoint 2010, for example:
I couldn’t find a solution to this problem until I found a post on the MDSN forums from one of the PowerPivotGeeks Dave Wickert:
All 3 of these options use the new content sync utility that allows asychronous uploads to the server.
And unfortunately it can be a bit buggy. I have found that it is OK with small files, but hangs quite frequently with large ones.Therefore I never use *any* of the 3 options — I always use the file upload feature in SharePoint. You go to the document library where you want the file to be loaded, and click on the “Document” ribbon. From there, you can upload the file to SharePoint. I have found this much more reliable and considerably faster (2X to 3X).
So don’t use the save as of publish functions but just upload the file within sharepoint. This solved my problems.