Manual compile

Is there any differences between manual compile and using synaptic when install xbmc and vdr?

depends on what branch you are compiling from. if you compile from the pvr-ppa tree, you'll get the same source as the source that's used to build the ppa package: https://github.com/opdenkamp/xbmc/tree/pvr-ppa

the master branch is under development, so unless you know what you're doing, you won't know what you'll get.