I'm on Inventor 2009 (as of today), but I had the same problem with 2008. I have a dimension style set-up like I want, but the "By Standard" pops up every time I select a dimension command. I want my dimension style to pop up every time I select a dimension style.
Try this in your drawing template:
Format/Style and Standard Editor
Click the + next to Object Defaults
Click on ObjectDefaults
In the Object Type column, find an object you would like to change. In the Object Style column, click on the current style for the object. Click the down arrow that appears next to the current style to see all of the available styles for that object and select the new default for the object. Do that for all the objects that you want to adhere to your standard, save and exit.