The electro-mechanical, multivane intensity modulated collimator ("MIMiC") slit collimator with 40 vanes has been applied in the delivery of inversely planned sequential tomotherapy to over 4,000 patients. The collimator is binary in that each vane switches between fully open or closed status. Resulting beamlet patterns provide the intensity distributions imparting dose to the patient. The bouncing and damping of vanes at the two ends of their travel cause transient dose perturbations near and at the borders of the treatment field. These perturbations are not explicitly modeled by the planning system. Clinical beamlet profiles and output factors may then differ from those in the planning system and as a function of the vane switch period. A mechanical model of vane switching was developed to describe this dependency. Dose output and distribution of seven simple vane patterns with different switch times were measured with ionization chambers and radiographic films in polystyrene and anthropomorphic phantoms. Linac output dependence on switch time relative to vane open time was determined for four intensity modulated radiotherapy (IMRT) patients from measurements of an ionization chamber embedded in a cylindrical polystyrene phantom. Results demonstrate output dependence on switch time and, accordingly, on the servo mechanism for monitor units, arc length, dose rate, and gantry speed. In conclusion, the output dependence borders on clinical significance-improvements to collimator, dose calculation, commissioning, and quality assurance (QA) are suggested.