Why can't I change the Memory Settings in Delta2D on a modern Windows system?

Although I am logged in as administrator, Delta2D says

Can not write memory preferences to 
C:\Program Files\DECODON\Delta2D\etc\delta2d.conf. 
Start Delta2D as an administrator.

How can that be?

This happens since with Windows Vista Microsoft introduced a new security mechanism, called User Account Control (UAC). This mechanism is meant to prevent users from damaging their system accidentally or unknowingly, and, as one consequence of it, even users with administrative rights do have to start programs explicitely as administrator if they want to run a program with elevated rights.

To run a program one time as an administrator

• Right-click the program that you would like to run as an administrator and select Run as administrator.
• At the User Account Control (UAC) dialog box, select Continue. After the user authorizes the elevation, the program will launch and run with the user's full administrative access token.

For more details about UAC please have a look at Microsofts Tech Net site, or for a brief overview see the Wikipedia article.