Thanks Wouter - just to add for anyone who is having this problem, if you are WAY off on your initial alignment you may not be able to see the little red "cross hair" that is mentioned in the instructions (the fact that there is also a purple set of cross hairs may even add to your confusion given the bug - as it did for me).
If this is the case, then you should use the purple cross hairs as a proxy for the red one you will se as you get closer to PA, what you need to do is;
1). do your three alignment photos as per the standard alignment process
2). when the results are computed you will see a PA error in degree/minutes/seconds - the SCALAR for this is accurate, the VECTOR is not (ie: the size of the error is correct, it's just telling you the wrong direction) - you will need to do the opposite of what is said on the instructions with regards to the pink line.
3). To help you guide, I recommend you position the cursor with the pink target finder/cross hairs somewhere on the screen as though there is an imaginary line that continues from the end of the pink line all the way down as far as you can go on your screen - for this reason it's usually best to double click somewhere on teh results screen to move the end of the pink line to create as much space as possible to create your "virtual line" (it will make more sense with screen shots i am sure - PM me if you need help).
IGNORE ANY INSTRUCTIONS ABOUT SELECTING A BRIGHT STAR, you will use your pink target icon to make your own virtual star
4). once you've done this (moved the pink line) click next and start refreshing as per the instructions - now move your mouse pointer over the results screens (where you can see the star field) and place BUT DO NOT CLICK) so that the pointer/target icon is floating on an imaginary vector that joins the tip of the pink line in one continuous line to wherever you place the pointer/target icon - this becomes your "virtual star"
5). now adjust your RA and DEC to get the tip of the pink line to move towards your "target" virtual star - remember we are doing this just so we can get the scope closer to the SCP/NCP so that we can see the little red target that Wouter mentions.
6). then follow Wouters inductions as above, the hardest part will be remembering to do the exact opposite and then of course to line up your star with the very end of the TINY little pink line, but it is possible to get within a few arc seconds with a little practice.
7). wait for the fix/workaround