I.E. If I live in one section of town and have a business in another when I go to a meet in that same section, why would I risk my fake SIN at the checkpoint when I can just use my legal one and get past with no problems. For now I just gave it to them for free as part of the SINner negative quality.
Red
And that situation sounds perfectly legit 
You must have misunderstood, my players are note trying to fool me or use there hindrances as advantages. We are a very story driven group. Backgrounds are an everyday part of that. We all go to great lengths to bring the story to life and knowing how you SIN ties you to the world is a part of that.
However
A) is this a Criminal SIN? If so, the guards are still going to give the PC grief whenever they go through the checkpoint, and will scan them for contraband much more regularly and thoroughly than Joe Average
B) is this a Civilian SIN? At which point when something Illegal pops up on a regular scan (which will happen eventually, due to Shadowrunners constantly having explosives residue, weird chemicals, firearms, or cyberware around them) then their Civilian SIN now becomes a Criominal SIN.... Yay! 
Explosive residue? Weird chemicals? Regular scan? if this is a regular scan then even a perk like a fake SIN will not get them by. The second one of these comes up, they would be screwed. I don't think that scans of this sort would be used in everyday traffic of millions of contrite trying to get to work in one of the largest corporate owned strutters in the world. Commerce would come to a scratching halt. People need to be able to walk by and at the most there pass would be checked. Those with black passes may be pulled out of line to face a chem sniff and mag scanner but not everyone. On a bad day they may start pulling at random but not every day.
Also having your SIN turned to a criminal one is the least of a runners worries in Manhattan.especially since that would happen if you where a SINner or not. The SINless in Manhattan are also worse of than the SINed as they are usually beaten in public to prove a point. Runners on the other hand have abetted chance at catching a break as they work for the corporations that own the city, but it still means a hefty bribe on a good day and a beating on a bad one if you are SINless. The ones with SINs get off with just having there SIN turned criminal? That would be a slap on the wrist if you asked me.
Unless the runner is BEHAVING like Joe Average on a regular basis, and carrying the equipment opf Joe Average (including permits for all cyberware as well as firearms), they're going to get some grief, and at the very least, asked for some 'Please Explains' regularly by the authorities...
It's a vicious Negative quality for a shadowrunner.... so while I applaud the PC's for wanting to flesh out the details, this quality should be more of a hindrance than a help (especially if Blood/Saliva/Sweat is left on a run... a SIN includes a full DNA markup, and if matched, will now advise that Joe Average regularly goes through Checkpoints A and B on their way to work.... )
At 5 points I wouldn't call it vicious, it is a negative one but not vicious. The problem with having a SIN is not having it one day turn negative, the problem is having it track you down. You see, every time you use a SIN real or fake you leave a trail. Fake ones can simply be burned, real ones can not. If I use the real SIN to pass the check point from a to b everyday then there is a trail of that. If I go in to buy something minor for a run there is a trail to that, if I use it to book a restaurant there is a trail of that, and the more I use it the bigger my nearly unburnable trail becomes. One minor slip on a job and a data search latter and my trail to me real life comes barreling down on me. One fingerprint, one skin flake, one hair sample and boom the Corp I just hit knows about me. Luckily my players are smart they play well and try to keep the authorities and corps at bay and when they do do a run they make sure that the payback is mitigated as much as possible.
They don't use regular amor they use stun spells they don't destroy corporate property you less any of that is unavoidable. You see corps care only about money and though you may have cost them some every family they have to pay pension to, every training dollar they have to spend on a replacement, every cent that have in repairs to a major facile, and every PR coverup they have to spin is a tick on the kill the runners and the people who hired them scale. It is inevitable that someone will wish payback but the amount can be negotiated.
But we may be running of track. After every game I add to a file I keep on every runner in the game. This file is the investigation report that those involved will actually do. If you mess up it will have reproductions in the game. The number of characters that have lost there lives due to weighting the scale mentioned above coupled with the DNA left behind that got the investigators onto the trail and the amount of times they used there free checkpoint pass to create the trail that got them killed makes me wonder why SINner is only 5 points. It should be much more. The only thing i can come up with is that its also has its perks. It will eventually get your charcter killed or force his early retirement though so it is a 5 point negative quality overall. This being said I still have players who wish to try and see how long they can last on that bull ride. Trust me it is a hindrance and I will let them have as much free rope as they wish to eventually hang themselves with but the story it creates as they try to survive the inevitable is worth it to Bo them and me.
As I said criminal SIN is the least of my players worry, this flaw will kill them. I think I finally found the cost, it just costs time in game, nothing more, well maybe 5-10 new yen for processing fees, the players have enough to worry about without needing a cost on top of that.
Red
