Quartus TCL vs Quartus GUI

This is not expected. Once you compile with Quartus (using any method), you should be able to load the resulting database with the Chip Planner.

I recommend you confirm that you are not accidentally using two different versions of Quartus (e.g. 8.1 to compile, abd 9.0 for the GUI). Also confirm that your scripts are not deleting anything. Maybe you can post your script.

You can also try with a new small design. The following three flows should be identical:

1.- From the GUI, click "play" button

2.- From command-line, type "quartus_sh --flow compile <name>" and then open Quartus and see report

3.- From tcl (I am typing from memory, so I may have the exact syntax wrong):

load_package flow

project_open <name>

execute_flow -compile

project_close

Then open GUI and open report