Hi everybody. This is my first post here.
I have been having the same problems as the OP here. I am using Xubuntu 12.04 and VMWare Player 4.04, both 64 bit.
I do not have a solution but I have discovered something very odd that nobody else has mentioned and which might help somebody more knowledgable than me to figure out a solution.
The key to the problem seems to be the file:
When I add new VMs to the library I can see them getting stored in this file.
When I log out and back in again the file is gone.
When I add new VMs to the library again the file is recreated and lasts until the next logout and login.
If I backup the file while it has VMs in it and then restore it manually after it gets deleted then the VMs reappear in the library, until the file gets deleted again.
Conclusion: Something, I have no idea what, is trashing the file ~/.recently-used.xbel on logout or login and this is why the library is lost after reboots.
Irony: Googling "recently-used.xbel" reveals that this file is not unique to VMWare but is used by other applications (although they keep theirs in ~/.local/share/recently-used.xbel) and most people asking about it are trying to get rid of it not retain it.
Is that any help? Does that give anybody a clue they can pick up and run with? It would be nice to get it fixed.
PS: I just went looking in /etc to see if anything there was trashing it. I didn't see anything but I did notice that Apparmor has rules relating to it. I don't know if that is any help?