I think I've found my solution.
I had copied the xml and changed the items originally myself. So I deleted it and created it through Eclipse (right click on the res/menu folder > New > Other > Android XML File > Menu). I no longer seem to be getting the appt.exe error. I then added the items using Eclipse instead of writing or copying them myself.
The only difference in the two files is that the old one ended each item with this:
\>
And the one created by Eclipse uses this at the end of an item declaration:
></item>
As for Eclipse not recognizing my xml files, AdamM helped me find the solution to that problem as well: 1) I deleted the R import
2) Commented out the lines that were giving me errors in recognizing my xml files
3) Restarted Eclipse & Built All