In which files did you find the ms-its links? They are related to chm and probably not needed for html alone.
Not sure about chm related, seems to be system, classes links. Here some numbers:
$ find lcl-from_chms/_build/ -type f | wc -l # --> 20225
$ ack -l "ms-its" lcl-from_chms/_build/ | wc -l # --> 7749
$ ack -l "ms-its:rtl.chm" lcl-from_chms/_build/ | wc -l # --> 7651
$ ack -l "ms-its:rtl.chm::/system" lcl-from_chms/_build/ | wc -l #5607
$ ack -l "ms-its:rtl.chm::/classes" lcl-from_chms/_build/ | wc -l #4169
Here an example from '$ vi lcl-from_chms/_build/forms/tcontrolscrollbar.clientsize.html':
<td><p><tt><span class="code"> <span class="kw">public</span> <span class="kw">function</span> <a href="../forms/tcontrolscrollbar.html">TControlScrollBar</a><span class="sym">.</span>ClientSize<span class="sym">: </span><a href="ms-its:rtl.chm::/system/integer.html">Integer</a><span class="sym">;</span></span></tt></p></td>
I'll go with the converted chm files. Just for the record, below the difference between the chm-converted and wget'ed. I cannot exclude that there was a problem with wget (albeit it looked reasonable and the missing files/folders might be newer and not yet available on the sourceforge online help?). Numbers:
$ find lcl-from_chms/_build/ -type f | wc -l # --> 20225
$ find lcl-wget/ -type f | wc -l # --> 17635