Relaxation time (T10) estimation using variable flip angle sequences is a key step for pharmacokinetic (PK) analysis of tumours in DCE-MRI exams. In this study, the effects of motion within flip angle sequences on the T10 and subsequent Ktrans and kep estimation were examined. It was found that errors in T10 estimation caused by motion had a significant impact on subsequent PK analysis. A new similarity metric, based on the T10 regression error, for groupwise motion correction of variable flip angle sequences is proposed and compared against Groupwise Normalized Mutual Information (GNMI). In rigid registration experiments on simulated data, the new metric outperformed GNMI, showing an improvement alignment of over 14% in terms of average target registration error, which is also reflected by a lower T10 estimation error. Finally, registration was applied to 46 clinical sequences to identify the average amount of motion found in this type of acquisition; this showed an estimated displacement of 0.98mm, which could lead to over 25% Ktrans estimation error if motion were not corrected.