FMCB itself didn't come with the apps you want. Like with your PC, phone etc, you can download whatever you want and copy it to your PS2.
One way to get a good, working copy of FMCB is to actually install it yourself. Hopefully with a good memory card.
You can actually use FMCB with your saves. There's no need to format it. Installing FMCB is not actually more risky than copying files to it, as that is what the installer really does - copy files over to the memory card.
It's not a 100% failure. What might actually be happening, is the modchip modifying some code in EE memory, that results in FMCB and/or some thing not working properly. All this, depends on the modchip (not whether it's a clone) and what's in EE memory.
A normal, clean PS2 doesn't have something extra like a modchip changing memory...
If you're using FMCB v1.8c and later, it did not support OSDSYS from the SCPH-10000 and SCPH-15000. This was one goal, when I proposed to add new features to FMCB.
What did you do? Power off?
I don't know how you're running SMS 2.9, but if you used my hack of it - I only got it working and didn't test all functions. Back in 2004, the perhaps the existence of the SCPH-10000 wasn't really known and/or people tend to write code for the PS2s they could find.
If you are using a normal, clean copy of SMS - SMS did not support the SCPH-10000/SCPH-15000 because it used some board-specific modules that are only present in the newer models.
It's not a problem with the console, but with how homebrew software was once commonly written.