The gist of the issue is that some apps, like Calculator in the Tools directory, do not load. There is an "attempt" as per the message on Workbench, but then nothing happens.
My set up is as follows:
Amiga 3000@25MHz, 2mb+8mb, stock. CF-IDE adapter attached to Acard 7720UW bridge which in turn is attached to the SCSI port. Using a Transcend 133x 4GB card. AmigaOS partition is 1gb, the other 3gb is Work.
I've installed 3.1.4 without any issues as well as the .1 update. The system boots just fine. The only thing is that some apps refuse to run, including Calculator.
The interesting bit is that I've got another setup, an Amiga 1000 w/ a Classic 520 and a SanDisk 8gb card. 3.1.4.1 works perfectly fine on it, including Calculator

I plugged in the 3k's Transcend into the 520 and booted the A1k up. The same behavior happened. The Calculator refuses to show up.
I then copied the Calculator file from the 3k's Transcend onto a floppy disk and rebooted the A1k with it's usual SanDisk 8gb card. The calculator loaded up fine from the floppy disk!
I took that disk back to my Amiga 3000 and plugged back the Transcend as well to boot it up.
Clicking on the Calculator icon on the floppy resulted in nothing, just as if I clicked on it from the Transcend. So no joy there.
I then booted my 3k with the 1k's SanDisk card. Lo and behold, the Calculator on the floppy and on the SanDisk loads up just fine!
So what's going on here?
It seems to not be an issue with the SCSI/drive controllers, since the behavior for the Transcend card happens on both the A1k and A3k.
I've also installed MMULib to see if that had anything to do with it as I was writing this and the same behavior persists.
Also, when attempting to load the Calculator in CLI, nothing happens, no error message, nothing.