I think this is the current question, but it's not obvious with the thread edits.
I simply have no idea why Spaceharrier (and possibly others) wouldn't be included in the list.
Any time a game that you're expecting in a list doesn't show up, do this:
1) create the all games list by hitting the button on the main UI.
2) locate the game in that new list
3) 2x click on that game and romlister will show you the XML for that game. There is probably something in that XML which you're telling romlister to filter OUT of your current list.
4) If you can't figure out what it is, post the contents of your -find: window here in a message and the XML for that game and I'll step you through it.
5) (optional) while you're in the "all games list" view, you can right-click on any game in that list and "throw" it into your working list. Useful really only for single games (like pacman) that you've filtered out but want to add in without changing your search criteria.
edit: also, posting this question in the software forum would have gotten my attention earlier, likely. i hang out there more...
edit2: my guess for why space harrier doesn't show up is that the control is tagged as:
<Controls>
<Control Name="Flightstick (Analog)">
<Constant Name="stick" />
<Button Name="P1_BUTTON1" />
</Control>
but there isn't actually a "flightstick" option for romlister's checkboxes, so those games were never getting pulled into your list. You can do this by getting your hands a little dirty:
In the -find: window, change the text that looks something like this:
& (joy2way | joy4way | !'control type=')
and change it to say this:
& (joy2way | flightstick | joy4way | !'control type=')
that is, insert the keyword "flightstick" into the list of acceptable controls you're looking for.