RTL simulation in ModelSim 6.1g Altera

This sounds like you have the full version of Modelsim (for which you don't have a valid license) on your path ahead of the AE version of modelsim (which you do). If you reorder your path, then you won't need to change directory before you simulate.

To change your path, right-click on My Computer and select properties. Click on the Advanced tab and then select Environment Variables at the bottom. Click on the path variable in either your User variables or System Variables and then click edit to modify it. Click OK and then restart MATLAB.