The focus of this study is on the Elekta XVI on-board cone beam computed tomography (CBCT) system. A rotational mismatch as large as 0.5° is observed between clockwise (CW) and counter-clockwise (CCW) CBCT scans. The error could affect non-isocentric treatments (e.g., lung SBRT and acoustic neuroma), as well as off-axis organs-at-risk. The error is caused by mislabeling of the projections with a lagging gantry angle, which is caused by the finite image acquisition time and delays in the imaging system. A 30 cm diameter cylindrical phantom with 5 mm diameter holes is used for the scanning. CW and CCW scans are acquired for five gantry speeds (360 to 120 deg./min.) on six linacs from three generations (MLCi, MLCi2, and Agility). Additional scans are acquired with different x-ray pulse widths for the same mAs. In the automated CBCT analysis (using ImageJ), the CW/CCW mismatch in a series of line profiles is identified and used to calculate the rotational error. Results are consistent among all linacs and indicate that the error varies linearly with gantry speed. The finite width of the x-ray pulses is a major but predictable contributor to the delay causing the error. For 40 ms pulses, the delay is 34 ± 1 ms. A simple solution applied in our clinic is adjusting the gantry angle offset to make the CCW one-minute scans correct. A more involved approach we are currently investigating includes adjustments of pulse width and mA, resulting in focal spot changes, with potential impact on image quality.