I've also got the same problem in SSIS 2012 VS 2010 TFS.
I do sort by name on the package node, project is checked out, check in, "No changes".
The packages are not sorted the next time I open the solution....
Also experience that packages does not get into the project-file for other TFS-users in our workgroup.
I also don't get the latest version downloaded even if I do Get specific/Get Latest/Overwrite.../Overwrite...
Which is a pain if you're not working alone in the project... :-( Packages/Connectors are getting lost, project files out of whack.
Anyone noticed the same thing and maybe got some input towards a solution for this?