Cannot embedd sqlite db to winforms application setup deployment

I have a winforms application in C# with an SQLite database. Everything works well when I run the application with Visual Studio (I'm using 2013). But when I use the visual studio installer and create a setup file and thereafter I install the application on my computer, the db is losing some tables or columns and hence the whole app doesn't work.

Any workarounds for this? Do I need to follow any rules or procedure when creating the setup or while embedding the .db file?