I'm afraid I can confirm this. I'm a software developer and use Eclipse 3.3.x with Java 6 in Mac OS X 10.5.x.

As a (hopefully temporary) workaround I eventually reconfigured some keys (the ones I use frequently) to work as expected in Colemak, that is define them with the QWERTY layout in mind. :-/
E.g. I often use the "Open resource" command (Command + Shift + R), which I had to redefine as Command + Shift + S (as the QWERTY S position corresponds to Colemak R position). Of course other shortcuts had to be redefined as well (e.g. Command + Shift + S is used for something else already), which is kind of a PITA.
Another thing I absolutely had to reconfigure was Command + S (save), which due to this bug produced a Command + D (delete line).

Added:
I just tried it again and found out that it works just fine with the Dvorak layout that comes standard with OS X (the regular Dvorak, not the Dvorak - Qwerty <Command>). So I assume it might have something to do with the Colemak.keylayout file after all. Unfortunately, the pre-installed keyboard layouts don't come in *.keylayout files - instead, they appear to be two binary files in

/System/Library/Keyboard Layouts/AppleKeyboardLayouts.bundle/Contents

- so there's no comparing Colemak.keylayout to another *.keylayout... :(

On Leopard 10.5.5 when using Microsoft Office and BBEdit (all Carbon apps), keyboard shortcuts in Colemak seem to work fine. Perhaps Apple have fixed this particular issue.