Potential differences in usage between CF and HDD?

[Mu.]

I've gone over my soldering several times (both reflowing and checking for continuity with a meter), and made sure every connection is solid. I've also been using Dragoncity's build of DS along with a clean install of DS with the 0.6.6 loader beta and both have similar results.

I have this issue with Crazy Taxi, Ready 2 Rumble and Shenmue, all of which are supposed to work with the settings in his spreadsheet.