I followed exactly the upgrade instructions and, to my disappointment, the download path continue to point to the old folder instead of the new folder. I thought it was the .htaccess, so I opened up the file and everything seems right. I contacted Dreamhost support and as usual, their quick support was quick and helpful. However, they can't trace the errors as .htaccess has no problem at all.

So today, I finally took some time out to go through the code and debug it. Guess what, it's in the DATABASE. The table prefix_DLM_DOWNLOADS stores the fix path to the filename, so the .htaccess has no effect and keep pointing to the old folder. Sigh, I have to manually edit every single row to point to the new folder.

What a waste of my time. For those who are still facing the problem, do check your database table and correct the path. Hope you did not waste your time like I did.