So this probably has something to do with the order in which the programs are hooking the keyboard handler (is that the right programming description? heh).
Thanks for taking time to write this report!
Your description is very very close to what a programmer would say. The programs are hooking the keyboard. When they hook the keyboard, they install a handler. The handler is the part of Mojo or HotkeyNet that does something (like execute a hotkey) when you press a key. And yes, the order matters.
What it boils down to is whether or not the program's handler allows other programs' handlers to see the keystroke. There is a chain of handlers, and each one makes a decision about whether the handlers that follow will see the keystroke. To control this with HotkeyNet, you include or omit <PassThrough> in a hotkey definition. Mojo allows other handlers to see the keystroke except when (1) broadcast is on and it broadcasts or (2) mouseoever is on and it's moused over.
The next handler can belong to the operating system itself. With HotkeyNet, for example, if you trigger a hotkey that doesn't contain <PassThrough>, HotkeyNet will execute the hotkey in response to your physical key press but the operating system won't do what it normally does when that key press happens.
All this behavior is by design. Its intrinsic to what people want these programs to do. If the progams always called the next handler in the chain of hooks, they wouldn't do their jobs.
With Mojo, I haven't yet fine-tuned exactly when it calls the next handler and when it doesn't, so you might have found something I should change.
I'm still wondering if you found something that's exclusive to the Enter key for some reason. There's no special code for that key and nothing that I wrote above applies to that key more than any other key.
If you want more help with this, I'll need to see the whole hotkey (not just the fragment you pasted).
With a workaround for this problem now (I think), at this point the main problem I've been having with the mouseover is that I get shift, alt, and ctrl (and other normal keys as well) 'stuck on' when I swap between PCs. It would be really nice to have a checkbox for a mode where all keys are released when you mouse over to a different PC (well, all virtual keys, I suppose it should just revert to the mode the local keyboard is in?)
I fixed this in a recent Mojo build for the case where it happens due to things such as Alt-tabbing on the local PC. It sounds like you found another situation where the fix needs to be applied. Could you give me a step-by-step procedure for making the problem happen?
But the mouseover control and functionality is top notch, you all did a really good job there - I'm able to right-click and drag in EQ2, which a few other programs I tried were not able to do successfully. The amount of updates needed and quality of control is there. Keep up the good work!

Thanks for the kind words! And thanks for taking time to write this report! Much appreciated.