It could be the amp or just a subtle effect. I don't have a lot of experience with the Marr Jaguars, but I can chime in on one thing...
Amplification makes a HUGE difference in how your Jaguar's controls are received. I have a Bugera 333XL, a Digitech RP-250, and a Fender MiniTone Master amp - out of the three, the most responsive to change of the Strangle switch is the Bugera (Tubes and 120 Watts), the least responsive to anything is the little 1W plastic battery powered mini Tone Master amp.
Another thing is the Series switch only affects the 4-way selector switch when it's in "Series" mode (which I think is all the way toward the neck, but don't quote me on that). So it won't have any effect on it in any other selection mode.