Like said above, the section access part has to be loaded first. The fact that this adds so much load time suggests to me that there are probably some synthetic keys being created between the access table and the application. These won't show in your table view as they are hidden. If you are linking on multiple fields, consider using composite keys. You can test your data model between access and application by commenting your section access statements to load the access table as a 'normal' table so you can look at the data model.
Sorry, but it does not matter where the Section Access is loaded. You can do it at first, at last or in the middle of a script. It's only important that it starts with a "SECTION Access;" and ends with a "SECTION Application;". Normally, there are no problems.
Maybe you have forgott the line "SECTION Application;" after your section access load?
I agree with Christian. There is no requirement to perform section access first. Its usually one of the last steps in the load script in most of my applications. Indeed, if you want to use generic keys in your section access, you can only build these keys after loading the model.
The only reason for loading SA first would be if you want to place it in the hidden script tab.
Logic will get you from a to b. Imagination will take you everywhere. - A Einstein