I haven't used Inventor since 2012 for my senior design project, but we did use the frame generator quite a bit; albeit round tubing. We had to create custom profiles as well, but rather than try to explain it, here is a quick video:
https://screencast.autodesk.com/Main...d-6368c49ecf18
I'm 99% positive the error you are running into is the fact the file is imported as a STEP (or dumb solid) file. In order for the frame generator to work, you have to define variables for Inventor to adjust. I think the video kind of shows this, but in the greatest detail; however it should be enough to get you started. Once you recreate the extrusion as a native Inventor part, you should be able to define the parameters to change. The tricky part will be getting the hole pattern to populate, as I have never attempted to something of this nature.
Hope this helps and let us know how it goes. I'm sure other teams could value from this resource.
EDIT Here is the link to the video that we used to as a reference to create our profiles, it is a little lengthy, but way more detailed than the link above:
https://www.youtube.com/watch?v=XOwR89pA_e8
After giving a little thought to the hole pattern, I'm fairly positive it cannot be added to this new profile you are going to create. I would recommend placing one hole on each of the desired faces and pattern the hole down the length of the tube.
/EDIT