The first things that comes to mind are:
1. The lifter bar might have some debris stuck to it such as bits of vinyl from sprocket holes. Make sure these are not present and that the lifter bar is clean. Adjusting the lifter bar is rarely the solution for the issue you are having. Proper adjustment of it should be just above touching the drum surface when lowered to maximum depth.
2. The chrome shafts, tool head, sprockets and sprocket slider are in need of cleaning and lubrication. The Gerber plotters are built like tanks but do need regular cleaning and lubrication to avoid erratic problems like you are reporting.
3. The pin feed sprockets require regular cleaning and removal of adhesive that accumulates at the base of the pins.
4. The condition and type of blade as well as the downforce being applied are very important. The blade should be a 30° blade for most vinyl cutting. Blades are made of carbide and are very brittle. They must be free of any chips which can only be seen under high magnification. When in doubt, try a new blade. The weight or downforce you use should be just enough to cut the film without cutting through the liner. It should just leave a slight mark in the liner.
There are links to a couple of Gerber documents that may help you:
http://www.gspinc.com/downloads/PDF/fastfacts/5262.pdf
http://www.gspinc.com/downloads/PDF/fastfacts/5256.pdf