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Are you creating a new Make Target with the same name as the project folder you created, then double-clicking the make file in the Make Target window?
For instance (assuming you are using SDK 2.0 and the new TAG3 board) in order to create a new project under /apps called myproject, first copy and paste one of the existing projects like automation_io, then rename the folder/project to something like myproject
Then, create a Make Target called myproject-BCM920737TAG_Q32 download. To do so, right click automation_io-BCM920737TAG_Q32 download and select copy. Now paste the same and rename it myproject-BCM920737TAG_Q32 download (needs to be entered exactly like this as the tool uses the naming structure as the path to the files).
Now double-click on the Make Target "myproject-BCM920737TAG_Q32 download"
This should work since all you really did was rename the automation_io project. You can now start modifying the code in the project you created to fit your application.
Note that this process is also partially described in the Quick Start Guide as well.
I believe the errors you are seeing occur when you highlight the project folder you created and use the Project menu at the top of the Eclipse GUI to initiate a build.