Just found this somewhat odd behavior, with, apparently, a quite restricted domain. The problem is that using comment_line overwrites the last few characters of the line with the end-comment delimiter. However, it only seems to happen in the following circumstances:
1. "At level of indent" is selected in comment line options
-AND-
2. The line begins somewhere between column 1 and the first indent level.
The following example illustrates:
<!--<div class="searchbox"><wiki:Include page="SearchBox.jsp" /></div>-->
<!--<div class="searchbox"><wiki:Include page="SearchBox.jsp" /></div-->
<!--<div class="searchbox"><wiki:Include page="SearchBox.jsp" /></di-->
<!--<div class="searchbox"><wiki:Include page="SearchBox.jsp" /></d-->
<!--<div class="searchbox"><wiki:Include page="SearchBox.jsp" /></div>-->
<!--<div class="searchbox"><wiki:Include page="SearchBox.jsp" /></div>-->
The first line is fine because it starts in column 1.
The next three lines get their tails lopped by the number of spaces between column 1 and indent level 1.
The last two lines are ok, with #5 starting at indent level 1 and #6 at level 1 + 1 column.
I wouldn't be surprised if there were other characteristics as well, but this is what I've managed to deduce after a couple days of headscratching.