Firstly, hello everyone... don't know why I've never found this before, as I've worked on-and-off with Amigas for the past 15 years. One of the interesting projects was the revival of an animated jigsaw puzzle program, which for the past eight years has been running successfully on two expanded A1200s in the Exscite part of Waikato museum.
So a bit of an introduction (skip to the problem below '----' if you like) - I've just finished un-towering my A1200

strange eh... I bought it in this giant ugly painted tower. I bought a Mediator for it five years back, whereupon it wouldn't fit in the tower - it's been strewn across the desk ever since. Mostly used to write disk images for games on my A500, especially since the Mediator stopped working a year ago (a mysterious custom-logic fault).
So recently I obtained an A1200 case/keyboard, dug out a Squirrel SCSI that I picked up a few years back, bought a SCSI CD-writer and found an external case for it, and in the last week I've set up my A1200. It has a Blizzard 1260 (with 40MHz 040), 32Mb RAM, and a CompactFlash IDE adaptor that I bought a fortnight ago, with a 2GB CF card.
For file transfers from my PC, I've used a CF card and a Verbatim CF-PCMCIA adapter - works brilliantly. Also the other day I've bought a 3Com Etherlink III, took me a number of goes to figure out why Miami couldn't open the device - turns out you have to disable the CF0: and Squirrel devices first!
So, onto the problem - which has me completely stumped!

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When I try to open programs off the CF 'hard drive' (2GB card with 2.5" IDE adapter, formatted as a hard drive), e.g. Voyager, everything results in "Unable to open your tool 'V'". That is, when I double-click the V icon, I get the 'unable to open' message. And the same for every single other application! This is not when I try to open a project (I know how to set a default tool) - this is when I try to open the tools themselves!
The programs/files were copied from a 3.5" hard drive onto a CF card (placed in a PCMCIA adapter mounted as CF0:), then the machine was rebooted with the CF hard drive, and the files copied from the CF card (CF0:) onto the CF hard drive.
Also, in case something went pear-shaped, I bought a 6GB 2.5" IBM hard drive, and copied all the programs/files from the same CF0: CF card onto the real hard drive too...
...and guess what? The programs open FINE from the 'real' 2.5" hard drive! The exact same files/programs that I copied to the CF hard drive...
So I think this is some sort of buffers-issue - also, when I write disk images to floppy, they don't work. I expect this is related. It's almost as though all files over a certain size are not readable. Everything that I've installed onto the CF hard drive from a CD (i.e. OS3.5 and its apps) is fine, though! e.g. I can run AWeb 3.1, but not Voyager.
Please let me know if anything jumps out at you or if perhaps other people have had a similar problem with a CF hard drive (I saw the excellent tutorial here a few moments ago - in fact, that's how I found this site).
Cheers,
-Alex