System Information
Win7 x64

Blender Version
Broken: Blender 2.69 r60995
Worked: Unknown

Short description of error

Whenever Undo is executed, all Python node trees in the current blend file lose their users. If they don't have a fake user this leaves them with 0 users, and as a result they are not not written to file.

Exact steps for others to reproduce the error

1. Create a Python node tree
2. Perform an action which creates an undo step
3. Undo
4. Observe user count of node tree

Example blend: