Potential differences in usage between CF and HDD?

[Mu.]

I've modded my Dreamcast with an IDE mod and custom BIOS, and I have to say it's been well worth the time and effort I've put into it. Being able to load all my games off a single storage device is something I look for in all my consoles and it was great to find out that it was achievable with the Dreamcast as well.

So far I've been using it with a SanDisk 50MB/s 16GB CompactFlash card plugged directly into a GD-IDE board with an adapter and have had decent compatibility with most games I've been wanting to play (e.g. Star Wars Racer, V-Rally, Toy Story 2), however some others just simply don't work with my system despite others users here being able to play them perfectly with the same configuration (the main ones in my case being Crazy Taxi, Ready 2 Rumble and Shenmue).

I've had Ready 2 Rumble boot and run perfectly on one occasion, but as soon as I took the CF card out and copied some more files it would refuse to boot again.

So my question for this thread: Should a CF card be functionally the same as an IDE hard drive when being used in a Dreamcast for DreamShell, or do some changes need to be made to obtain the same compatibility? I've found a 40GB IDE laptop drive and a cable which I might end up switching to once I find a way to transfer files, but for now I thought I'd ask.

Just for completion, my console is a PAL VA1 (HKT-3030) converted to NTSC using DS' Region Changer. And switching it back to PAL didn't seem to make a difference.