When processing a file that happens to have the SSI version of 'include' in it, the velocity engine breaks.
There are many cases where we end up with files that contain both, before they are cleaned up.
Essentially, if it sees that syntax, it needs to ignore the include. A suggestion would be to check for any amount of whitespace after the #include, and then "file=". I don't think that will step on proper Velocity include syntax.