It's an issue with the XBMC plugin I believe, since it's not actually a keypress, but an event going through the XBMC api.
The workaround to this is to use the keyboard functions inside EventGhost instead.
That was how I ended up getting around it. I saw a few other posts that mentioned this but no one posted exactly how to do this. I eventually figured it out (it wasn't hard, but hey, I'm a newbie to all of this.)
In event ghost I started with a new blank configuration. I added a folder to keep all of the emulated keyboard functions in. Then I used the Add Macro\Window\Emulate Keyboard function to add each individual keyboard event. Then you add the MCE Remote plugin and associate the appropriate key press with the emulated keyboard mapping you want. I found this list of windows keyboard shortcuts which also helped.
<arrow keys> - navigate
<page up and down> - scroll up and down
<enter> - select
<esc> - previous menu
<backspace> - go up back (or up) a directory
<space> - pause
<period> - Skip Next
<comma> - Skip Previous
<tab> - Minimize Video
<backslash> - Full Screen Toggle
<printscreen> = Screen Shot
<minus> - Volume Down
<plus> - Volume Up
<0 - 9> - 0 through 9
p - Play
f - Fast Forward
c - Context menu
r - Rewind
x - Stop
m - Player controls
s - Shutdown menu
i - Info
q - Queue
z - Change aspect ratio
The only keyboard function I wanted that I didn't find was for mute, and for that I added the xbmc plugin to event ghost and mapped my mce mute remote button to it.
Oddly the remote response seems to be slightly better/faster doing it this way rather than using the xbmc plugin alone. Hopefully this will help others suffering from the same problems.