If changing the routing or location of the coax changes SWR then you have one of two issues. Essentially the easy description for both of these is you have antenna currents flowing at places you don't want them.
The most common cause is common mode currents. A lot of people will falsely insist that this isn't an issue with mobile setups, however, this is especially common with magnet mounts, especially smaller magnet mounts such as the one that comes with the Little Wil. As mentioned above, the magnet is to small in this case to properly "ground" the antenna to the vehicle below. In this case size (of the magnet) matters. Also, running a ground wire from the magnet mount to somewhere else on the vehicle is not a fix for this, RF grounds do not work that way and need to be as close as possible to the antenna. When it comes to CB frequencies, a two feet lead to a ground is enough to start effecting the tune of the antenna noticeably, and when you have a known problem like this if it appears to help the problem but in reality said problem still exists and is being hidden it.
The fix for this is to have an RF choke on the coax, the best place is right next to the antenna. The next best option is a few feet away from the antenna right after the coax enters the cab, but this should be no more than two or three feet up the coax. Where on the coax said choke is matters, and the further away you get from the antenna the less effective it will be. Do not assume that a random coil of coax (or figure eights in this case) will act as a choke, clearly in this case it is not. RF chokes are far more specific than that. Using ferrite to create said choke is also an option (many of us would say better option) here especially since they can be made much smaller and potentially hidden more easily.
Some people actually try to use said common mode currents to "tune" mobile antennas, and then typically think the problems such a "tuning" method creats as not being related to said "tuning". After all, they got a perfect SWR match right???
The other cause of this type of issue is something called a ground loop, although when it comes to magnet mounts this is far far less common due to how the magnet mount works. In this case, their are two or more "ground" paths between the radio and antenna of different electrical lengths. The only way I can see this happening when it comes to magnet mounts is if you have a ground wire running from the mount to somewhere else on the vehicle in an effect to "ground" said antenna. You will note I put the word "ground" in quotes. The reason is all to often in RF the reality of what a ground is and how it works is different than the DC centric ideas most people have on grounding.
The DB